The ID Update

by Denyse O'Leary
ARN correspondent

Not 98% or 99%, as every motor mouth on Hoax TV can tell you, between 9-11 hair fixes.

A friend writes to say:

In 2008 I made the prediction (based on data available from the draft chimpanzee genome) that the human and chimpanzee genomes were about 70% the same overall. This has now been confirmed for the Y chromosome in a detailed study.

The study found

As expected, we found that the degree of similarity between orthologous chimpanzee and human MSY sequences (98.3% nucleotide identity) differs only modestly from that reported when comparing the rest of the chimpanzee and human genomes (98.8%)15. Surprisingly, however, >30% of chimpanzee MSY sequence has no homologous, alignable counterpart in the human MSY, and vice versa (Supplementary Fig. 8 and Supplementary Note 3).

In aggregate, the consequence of gene loss and gain in the chimpanzee and human lineages, respectively, is that the chimpanzee MSY contains only two-thirds as many distinct genes or gene families as the human MSY, and only half as many protein-coding transcription units (Table 1).

He cautions that the authors of the Nature paper do not think that their findings for the Y chromosome are true for the whole genome.

Perhaps not, but it is nice to see sane people working on genetic similarity issues for once.

The paper is: Chimpanzee and human Y chromosomes are remarkably divergent in structure
and gene content, Nature 463, 536-539 (28 January 2010) | doi:10.1038/nature08700

The human Y chromosome began to evolve from an autosome hundreds of millions of years ago, acquiring a sex-determining function and undergoing a series of inversions that suppressed crossing over with the X chromosome1, 2. Little is known about the recent evolution of the Y chromosome because only the human Y chromosome has been fully sequenced. Prevailing theories hold that Y chromosomes evolve by gene loss, the pace of which slows over time, eventually leading to a paucity of genes, and stasis3, 4. These theories have been buttressed by partial sequence data from newly emergent plant and animal Y chromosomes5, 6, 7, 8, but they have not been tested in older, highly evolved Y chromosomes such as that of humans. Here we finished sequencing of the male-specific region of the Y chromosome (MSY) in our closest living relative, the chimpanzee, chieving levels of accuracy and completion previously reached for the human MSY. By comparing the MSYs of the two species we show that they differ radically in sequence structure and gene content, indicating rapid evolution during the past 6 million years. The chimpanzee MSYcontains twice as many massive palindromes as the human MSY, yet it has lost large fractions of the MSY protein-coding genes and gene families present in the last common ancestor. We suggest that the extraordinary divergence of the chimpanzee and human MSYs was driven by four synergistic factors: the prominent role of the MSY in sperm production, ‘genetichitchhiking’ effects in the absence of meiotic crossing over, frequent ectopic recombination within the MSY, and species differences in mating behaviour. Although genetic decay may be the principal dynamic in the evolution of newly emergent Y chromosomes, wholesale renovation is the paramount theme in the continuing evolution of chimpanzee, human and perhaps other older MSYs.

Did you get that? “Wholesale renovation.” No doubt there’ll be more real news to come.

But don't expect to hear it from Hoax TV. 70%? Doesn't quite have the same ring as 99%, does it.

Denyse O'Leary is co-author of The Spiritual Brain.

By Robert Deyes
ARN Correspondent

Shattered assumptions, broken rules and overturned beliefs. The science media seems eager these days to emphasize science's capacity to shift paradigms. And it was such a handful of descriptives that was used to convey the implications of a new study that redefines our view of genome architecture (1). At the heart of such excitement lay a tunicate organism called Oikopleura dioica that carries in its genetic armory "several peculiarities" (1). Weighing in with its 70 million base pairs of DNA Oikopleura is today venerated as the animal with the smallest known genome (1). But what stands out for biologists who have dedicated years to unpacking Oikopleura's treasure box genome is the 'odd ball' physical location of many of its genes (1). The Scientist's Megan Scudellari remarked that "Oikopleura's genes appear to have been shuffled like a deck of cards" (1).

At the apex of this presumed shuffling is that all-elusive but much loved patch-all process called evolution. "UV rays and other mutagens" that bombard Oikopleura as it ekes out its existence just below the ocean surface are the suggested deck dealers of this particular shuffle (1). But apart from this rather misty association between cause and effect, there is precious little in the evolutionary inferences of this study to satisfy an appetite for robust scientific argumentation. To be fair, there are observable facts that we can latch onto and embrace as the products of rigorous science:

(i) Oikopleura's genome is extremely small containing the same number of genes found in humans (18,000) but compacted into a genome that is 1/40th of the size (1). Genome compactness is reflected in small intergenic distances (53% are less than 1Kb)(2).

(ii) While the Oikopleura external phenotype is clearly in line with that observed in other tunicates, the intronic organization of its genome is vastly different (introns are very small peaking at 47 base pairs in length)(2).

(iii) Oikopleura is unique amongst the tunicates in having both male and female individuals (2).

(iv) Oikopleura exhibits high mutation rates and low dN/dS ratios per each 4-day long generation (dN and dS being the rate of substitutions in non-silent and silent sites respectively)(2).

But there is also fact-less guesswork. For example, since this new study found that many of Oikopleura's introns display high sequence homology, the follow-on assertion put forth by the authors is that introns multiplied in the genome in a hap stance, 'by chance' fashion and that genome architecture across the animal kingdom is therefore inherently plastic and unconnected to morphological/developmental complexity (1,2). Such a grossly overstated endpoint does not appear to be supported by anything close to a thorough examination of intron location and animal morphological variability.

Twenty years ago scientists began to understand the intimate role that introns play in gene regulation in higher order animals (3). We now know that intron splicing involves "the precise deletion of an intron from the primary transcript" so that exons on either end can be joined in readiness for protein translation (4). The choice of specific splice sites depends on the surrounding sequence and structure of the RNA (5). Three types of sequence- the 5' splice site, the 3' splice site and a branchpoint sequence- are almost invariably found in pre-mRNA introns of higher eukaryotes although these elements alone are insufficient to account for the specificity of the splicing reaction (5). Additional signals in abutting exons not only ensure that accurate splicing is maintained but also prevent exon 'skipping', which would of course adversely impact the functionality of the translated product (6).

In some cases more than one mRNA can be coded for by a "single stretch of DNA" as a result of different splicing pathways, different intron cleavage sites and selectively active promoters (3). The mouse salivary amylase gene is perhaps the archetypal example of the multi-variant role that introns play in gene regulation. In this instance alternative but nevertheless nucleotide-specific splice sites are used depending upon whether expression is required in salivary glands or the liver (3). Stephen Meyer writes: "like Russian dolls stored within Russian dolls, exons and introns encode multiple genetic messages within themselves and are themselves part of a larger genetic message" (7).

Genomic mapping has shown that "of 5589 introns mapped by interspecies protein alignments, 76% had positions unique to Oikopleura" (2). It is therefore assumed evolutionarily speaking that Oikopleura's single major spliceosome made up of U1 snRNP and U2AF proteins is capable of recognizing donor and acceptor sites in the genome and shuffling introns around accordingly (2). Such a proposed transposition and propagation seems to fly in the face of what we know about the contextual requirements of intron splicing as outlined above. For instance, if differing intron splicing pathways are active in distinct parts of an organism then we would expect their transposition to novel genome sites to be extremely disruptive to gene function within their new context.

Evolutionists' intron-splicing magic is rife with factless guesswork. Even the briefest of considerations as is offered here makes that plain.

Further Reading

1. Megan Sculellari (2010) Who Needs Structure Anyway? The Scientist, 18th November, 2010, See http://www.the-scientist.com/news/display/57814/
2. France Denoeud et al (2010) Plasticity of Animal Genome Architecture Unmasked by Rapid Evolution of a Pelagic Tunicate, Science, Vol 330, pp.1381-1385
3. Benjamin Lewin (1990), Genes IV, Oxford Cell Press, pp.484-486
4. Christopher Wills (1991) Exons, Introns & Talking Genes: The Science Behind The Human Genome Project, Oxford University Press, Oxford UK, p.112
5. Adrian Kramer & Tom Maniatis (1990) RNA Splicing, in Transcription And Splicing, Eds B.D. Hames & D.M. Glover, IRL Press, Washington DC, pp.141-145
6. Ibid. p.159
7. Stephen Meyer (2009) Signature In The Cell: DNA And The Evidence For Intelligent Design, Harper Collins Publishers, New York, p.463

By Robert Deyes
ARN Correspondent

Buried in the most recent scientific literature there is a story of love, sex, and intrigue that has all the makings of a hearty Mills & Boon novel. The central characters of this plot are not lovers wrapped in each others arms but fruit flies that choose their sexual partners according to the microbiota that line their guts (1,2). Lactobacillus plantarum is the 'cupid gut bug' that seems to have greatest influence on sexual preferences (1,2) And it appears to do so by influencing the release of a class of Drosophila pherormones known as cuticular hydrocarbons (1,2). For evolutionists this finding is cited as one possible avenue through which speciation might take place in Drosophila (1,2). For those of us who are critical of such work however there exists one small but important catch. That is that the sexual preferences observed are easily eradicated by simply treating fruit flies that have been raised on different diets, with antibiotics (1,2). In other words, no genetic changes that would ensure irreversible reproductive isolation, and hence speciation, have taken place.

The late paleontologist Stephen Jay Gould was convinced that for speciation to occur, so-called peripheral populations would simply have to become 'locked up'- isolated from the gene flow of their larger ancestral stocks- in such a way that new adaptations would become stable and not watered down by interbreeding (3). Gould's close colleague Niles Eldredge posited that new species could form, "by the mere accumulation of genetic differences in the two segments of a single ancestral species" on the basis of some sort of hypothetical, (however slight) change in the reproductive system (4, p.116). As he went on to add, "some modification of the reproductive system is required for speciation to occur" (4, p. 121).

Unfortunately for Gould and Eldredge such an exit glossed over key mechanistic questions. After all what mechanism could we come up with that ensured irreversible reproductive isolation from ancestral stocks? Attempts to correlate speciation events with some sort of unguided change in the genetic makeup of an isolated population have proved largely unfruitful. In their studies on fruit flies Laura Reed and Therese Markow suggest that reduced sperm motility as well as sperm storage, recovery from storage, or ability to penetrate the micropyle might play an important role in the hybrid incompatibility that results from interspecial crossings (5). But they readily admit that the lack of a known genetic causality for speciation today represents "a major challenge to evolutionary biology" (5). They further add that "no study has yet characterized levels of naturally occurring variation for factors causing postzygotic isolation in any animal taxon" (5). Such a challenge is of fundamental importance if, as Darwin did, evolutionary biologists are to confidently claim that speciation is merely an extension of population variation.

Today some scientists have posited that a small number of genes in individual species might somehow maintain populations as reproductively isolated units. Biologist Daniel Barbash and his colleagues from Cornell University put forward a gene called "Hybrid Male Rescue" (hmr) as a possible candidate speciation gene in fruit flies (6,7). They demonstrated that hmr was responsible for hybrid incompatibility between different species, seemingly acting in concert with an unknown autosomal factor (7). Yet they also recognized that the 13% interspecial amino acid divergence observed in the HMR DNA Binding protein was a tall order for "relaxed selective constraints" to have achieved on their own (7). According to their statistical analysis of mutational frequencies and in line with the Dobzhansky-Muller (D-M) speciation model, they were adamant that some sort of positive selection must have been at work although they were unable to suggest what selective pressures might have acted to favor reproductive isolation (6,7).

Darwin himself recognized that whatever factors might be involved in ensuring reproductive isolation they could not have arisen through natural selection. He wrote in The Origin of Species that "the sterility of species when first crossed, and that of their hybrid offspring, cannot have been acquired...by the preservation of successive profitable degrees of sterility" (8, p.361). As he subsequently noted "it could clearly have been of no advantage to such separated species to have been rendered mutually sterile, and consequently this could not have been effected through natural selection" (8, p.379). In other words whatever genetic factors had maintained reproductive isolation would have had to have been found purely through chance alone- a blind walk through genetic space in search of those mutations that would prevent reproduction between some individuals and allow reproduction between others (9).

Rather than supporting evolutionist dogma the picture of coordinated changes being effected in individuals numerous enough so as to ensure the creation of novel species resonates more closely with the tenets of intelligent design. It is the height of irony that evidence-lacking meanderings over evolution and speciation should become most apparent in the 'gut feelings' of the humble fruit fly.

Further Reading

1. Jeff Akst (2010) Gut Bugs Affect Mating, The Scientist, 15th December, See http://www.the-scientist.com/news/display/57793/
2. Gil Sharon, Daniel Segal, John M. Ringo, Abraham Hefetz, Ilana Zilber-Rosenberg, Eugene Rosenberg (2010) Commensal bacteria play a role in mating preference of Drosophila melanogaster, Proc Natl Acad. Sci USA Vol 107, pp. 20051-6
3. Stephen Jay Gould (2002) The Structure of Evolutionary Theory The Belknap Press of Harvard University, Press Cambridge, Massachusetts, pp.800-802
4. Niles Eldredge (1985) Time Frames: The Rethinking of Darwinian, Evolution and the Theory of Puctuated Equilibria, Published by Simon and Schuster, New York
5. Laura Reed, Therese Markow (2004) Early events in speciation: Polymorphism for hybrid male sterility in Drosophila, Proc Natl Acad. Sci USA Vol 101 pp. 9009-9012
6. A Gene Responsible for Hybrid Incompatibility in Drosophila, PLoS Biology Vol. 2, Issue 6, p. 709
7. Daniel A. Barbash, Philip Awadalla, Aaron M. Tarone (2004), Functional Divergence Caused by Ancient Positive Selection of a Drosophila Hybrid Incompatibility Locus, PLoS Biol. 2004 Jun;2(6):e142.
8. Charles Darwin (1859) The Origin of Species By Means of Natural Selection Or The Preservation of Favored Races In the Struggle For Survival Modern Library Paperbacks Edition (1998), New York
9. Darwin stipulated that in order for speciation to have segregated populations into reproductive isolates, so-called "disturbances" in the genetic makeup of offspring must have occurred whenever there were crossings between species. But natural selection could not have been the mechanism that led to hybrid incompatibility. Since natural selection favors those traits that are advantageous to an individual within a population, what advantage could be gained from one individual becoming reproductively isolated from the rest of its neighbors? Without the ability to reproduce no genes would be carried over to successive generations. Several individuals would have had to evolve their speciation genes in precisely the same way as to give a genetic constitution that was sexually compatible, this through chance alone.

One of the lasting contributions of Professor Phillip Johnson has been his stress on clarifying the meaning of the word "evolution". He found a variety of definitions in common use, ranging from the "alteration in allele frequency" (which makes everyone an evolutionist), to the all-embracing concept of evolutionism (philosophical naturalism). Debates about the relevant science are muddied by people failing to use the word "evolution" in a consistent manner; for example, the industrial melanism of the peppered moth is often cited as proof of Darwin's theoretical model of evolution by natural selection. In his book, The Edge of Evolution, Professor Mike Behe put great stress on understanding Darwinian mechanisms at a molecular level. It is not good enough to talk about adaptation at a phenotypic level because the mechanisms relate to molecular changes at the genotypic level. When the evidence is examined from that perspective, it becomes clear that Darwinian mechanisms cannot build complexity. In a detailed review paper, Behe makes this point again and proposes the "First Rule of Adaptive Evolution" to summarise the findings of experimental evolution.

Phenotypic change does not necessarily map onto genotypic change (source here)

To qualify for Behe's review, experimental studies of evolution must have involved adaptation and must have included an analysis of genomic changes at the molecular level. He has set out to classify the mutations associated with adaptive change. Significant data matching these criteria relate to bacteria and viruses.

"Since species can evolve to gain, lose, or modify functional features, it is of basic interest to determine whether any of these tends to dominate adaptations whose underlying molecular bases are ascertainable. Here, I survey the results of evolutionary laboratory experiments on microbes that have been conducted over the past four decades. Such experiments exercise the greatest control over environmental variables, and they yield our most extensively characterized results at the molecular level."

The details of the review are of a technical nature and are best read in the paper. There is originality in the perspective Behe brings, because many of the researchers responsible for the experimental work have not discussed whether the mutations lead to a gain, a loss, or a modification of functional features. At this point it is worth referring to FCTs, which is the adopted acronym for Functional Coded elemenTs. Behe's analysis of both individual and aggregated findings represents a significant contribution to the literature.

"As seen in Tables 2 through 4, the large majority of experimental adaptive mutations are loss-of-FCT or modification-of-function mutations. In fact, leaving out those experiments with viruses in which specific genetic elements were intentionally deleted and then restored by subsequent evolution, only two gain-of-FCT events have been reported: the development of the ability of a fucose regulatory protein to respond to d-arabinose, and the antibiotic gene capture by f1."

This is a striking finding and it deserves to be formally labelled. Behe has obliged us by suggesting "the First Rule of Adaptive Evolution". This is a descriptive heuristic (rather than a prescriptive law). Adaptive evolution has the effect of breaking or blunting any FCTs whose loss would yield a net fitness gain.

"It is called the "first" rule because the rate of mutations that diminish the function of a feature is expected to be much higher than the rate of appearance of a new feature, so adaptive loss-of-FCT or modification-of-function mutations that decrease activity are expected to appear first, by far, in a population under selective pressure."

The key point to note here is that this Rule is driven by empirical data rather than by theory. The Rule expresses the findings of intensive research and it informs us about what actually happens. It is not a prediction deduced from theory.

"Except in cases where specific genetic features were first removed, as well as in the case of antibiotic gene capture by f1, all adaptive mutations in laboratory evolution experiments with viruses seem to be loss-of-FCT or modification-of-function mutations. Thus, in general laboratory evolutionary situations (that is, where a microorganism was under a general selective pressure rather than a specific one), adaptive loss-of-FCT or modification-of-function mutations were always available. This cannot be said for gain-of-FCT mutations."

For those familiar with The Edge of Evolution, this puts the spotlight again on the challenge of building complexity. These empirical results show that the great majority of cases of adaptive evolution involve either loss of functionality or a modification of an existing function. Adaptive evolution pre-supposes complexity. There is little evidence to support a model of the origin of species using the mechanisms of random mutation and selection (whether artificial or natural).

"Leaving aside gain-of-FCT for the moment, the work reviewed here shows that organisms do indeed adapt quickly in the laboratory - by loss-of-FCT and modification-of-function mutations. If such adaptive mutations also arrive first in the wild, as they of course would be expected to, then those will also be the kinds of mutations that are first available to selection in nature. This is a significant addition to our understanding of adaptation."

As this paper has been subjected to much critical scrutiny, it is appropriate to add some pointers to help general readers with their own appraisal of its significance. First, some complimentary comments from critics about the way the review has been conducted:

"My overall conclusion: Behe has provided a useful survey of mutations that cause adaptation in short-term lab experiments on microbes." (Professor Gerry Coyne, Department of Ecology and Evolution at the University of Chicago, source here).
"I read the paper in draft form some months ago and have not re-read it, but even then it exhibited an impressive command of the experimental evolution literature, at least the literature on adaptation of whole genomes of bacteria and phages (as opposed to the 'directed' evolution of genes on plasmids and of naked nucleic acids). I consider MB's characterization of most molecular evolution in these experiments as point mutations and/or deletions to be accurate. [. . .] My own view of the MB paper is that it has done a service to the study of evolution by pointing out where the next generation of experiments should focus." (Professor Jim Bull, Section of Integrative Biology, University of Texas at Austin, source here).

Numerous objections have been raised to Behe's analysis. It is claimed that the experimental evolution in laboratories does not represent the real world because there has not been enough time. It is claimed that studies of bacteria and viruses do not properly represent the incidence of 'gain-of-FCT mutations' in eukaryotes. It is claimed that mutations involving horizontal genetic transfer and gene duplication need to be considered to do justice to contemporary evolutionary theory. These objections are addressed here, here and here by Behe.

This blog started by pointing out the strong empirical emphasis which Behe brings to the field of evolutionary biology. There is typically a reluctance of researchers to get to the falsification stage of scientific enquiry. Often, theory is elevated above experiment, because the theory 'must be true'. What we now need are a set of review papers showing how theoretical ideas such as horizontal genetic transfer and gene duplication fare when they are analysed experimentally. Scientists should welcome this public scrutiny of favoured ideas - because this is the only way we can escape from 'normal science' in the Kuhnian sense. But for the present, we should digest the findings of Behe's review - here is his summary of the take-home message:

"The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. [. . .] Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent."

Experimental Evolution, Loss-of-Function Mutations, and "The First Rule of Adaptive Evolution"
Michael J. Behe
The Quarterly Review of Biology, December 2010, 85(4), 419-445.

Abstract: Adaptive evolution can cause a species to gain, lose, or modify a function; therefore, it is of basic interest to determine whether any of these modes dominates the evolutionary process under particular circumstances. Because mutation occurs at the molecular level, it is necessary to examine the molecular changes produced by the underlying mutation in order to assess whether a given adaptation is best considered as a gain, loss, or modification of function. Although that was once impossible, the advance of molecular biology in the past half century has made it feasible. In this paper, I review molecular changes underlying some adaptations, with a particular emphasis on evolutionary experiments with microbes conducted over the past four decades. I show that by far the most common adaptive changes seen in those examples are due to the loss or modification of a pre existing molecular function, and I discuss the possible reasons for the prominence of such mutations.

by Denyse O'Leary
ARN correspondent

Just wondering. Have you seen examples from recent textbooks that match these examples from the 1990s through 2001?:

From Joseph S. Levine and Kenneth R. Miller, Biology: Discovering Life (D.C. Heath and Co., 1st ed. 1992, p. 152:

Darwin knew that accepting his theory required believing in philosophical materialism, the conviction that matter is the stuff of all existence and that all mental and spiritual phenomena are its by-products. Darwinian evolution was not only purposeless but also heartless--a process in which the rigors of nature ruthlessly eliminate the unfit.

Suddenly, humanity was reduced to just one more species in a world that cared nothing for us. The great human mind was no more than a mass of evolving neurons. Worst of all, there was no divine plan to guide us.

(My source tells me that this language was not removed for the 2nd ed. in 1994.)

From Douglas Futuyma, Evolutionary Biology (1998, 3rd Ed., Sinauer Associates), p. 5:

Darwin showed that material causes are a sufficient explanation not only for physical phenomena, as Descartes and Newton had shown, but also for biological phenomena with all their seeming evidence of design and purpose. By coupling undirected, purposeless variation to the blind, uncaring process of natural selection, Darwin made theological or spiritual explanations of the life processes superfluous. Together with Marx's materialistic theory of history and society and Freud's attribution of human behavior to influences over which we have little control, Darwin's theory of evolution was a crucial plank in the platform of mechanism and materialism…"

From William K. Purves, David Sadava, Gordon H. Orians, H. Craig Keller, Life: The Science of Biology (2001, 6th Ed., Sinauer; W.H. Freeman and Co.), p. 3:

Adopting this view of the world means accepting not only the processes of evolution, but also the view that the living world is constantly evolving, and that evolutionary change occurs without any ‘goals.’ The idea that evolution is not directed towards a final goal state has been more difficult for many people to accept than the process of evolution itself.

Hat tip Stephen E. Jones

Denyse O'Leary is co-author of The Spiritual Brain.

by Denyse O'Leary
ARN correspondent

In Science , we read:

Altering the Past: China's Faked Fossils Problem

Richard Stone

Specialists and collectors around the world have long decried the flood of sham fossils pouring out of China. But Science has learned that many composites and fakes are now finding their way into Chinese museums, especially local museums. One paleontologist estimates that more than 80% of marine reptile specimens now on display in Chinese museums have been "altered or artificially combined to varying degrees." One consequence of the fakery is an erosion of trust in museums, which are supposed to enlighten—not con—the public. Scholars, too, pay a price: They waste time sifting authentic specimens from counterfeit chaff. And a genuine blockbuster fossil can be destroyed by attempts to enhance its appeal. (Caution: Subscriber wall)

Besides which, the past can be faked to support whatever thesis an establishment likes ...

It is high time many became more critical of museums. As Michael Ruse writes*,

Evolution after Darwin had set itself up to be something more than science. It was a popular science, the science of the marketplace and the museum, and it was a religion—whether this be purely secular or blended in with a form of liberal Christianity.

*For an informative account of the role of museums in the spread of evolution as
a religion, see Michael Ruse, The Evolution Wars: A Guide to the Debates (Santa Barbara,
CA: ABC-CLIO, 2000), pp. 103–05. For his own ambivalent view, see pp. 113–14.

Denyse O'Leary is co-author of The Spiritual Brain.

Although it is common to hear references to the "Cambrian explosion", no-one who uses that expression thinks of it as an instant in time when the fuse was lit and - ZAP! - the phyla were born. It has always been recognised that some phyla appear stratigraphically later than others. The problem for Darwin was that the abrupt and early appearance of phyla in the fossil record did not fit his branching pattern of gradual evolution: his model extrapolates from diversification at the species level to produce the larger taxonomic categories. The different phyla should appear after, not before, extensive speciation. A detailed review paper has recently been published which has much useful information about the data relating to the Cambrian record of animals, but which unfortunately mixes this up with highly contentious interpretation. The authors introduce the issues in this way:

"These observations (of the great radiation of animal life during the Early Cambrian) led scientists to focus in particular on two puzzling aspects of the Cambrian radiation, both encompassed by the term "Cambrian explosion". The first is the dramatic increase in disparity (morphological distinctness) as represented by the supposed appearance of nearly all major animal body plans (equivalent to the animal phyla) within a geologically brief interval of time near the beginning of the Cambrian. This problem was compounded by an apparent lack of evidence for "intermediate" taxa - taxa that lie close to the last common ancestor of different phyla in the metazoan tree. The second difficulty is the high rate of diversification (increase in number of species) in the Early Cambrian, particularly the apparent spike in diversification during the Tommotian and Atdabanian ages, spanning an interval that seemed short relative to subsequent radiations."

"The big question that the Cambrian Explosion poses is where does all that new information come from?" says Dr. Stephen Meyer, a featured expert in the documentary. (source here)

Focussing on the analysis provided of the fossil record, the authors select sites that provide opportunities to do detailed stratigraphical work: in Morocco, Siberia, Mongolia and China. Much of the paper is devoted to fossil appearances and chemical isotope analyses drawn from these localities. They give particular attention to the small shelly fauna that characterises the Early Cambrian (the lowest two stages are the Nemakit-Daldynian and the Tommotian). A strong link is found between fossil appearances and seawater chemistry. This is their summary:

"The time line of small shelly fossil first appearances indicates the following.
(1) All aragonitic taxa appeared in the Nemakit-Daldynian, before the first appearances of calcitic taxa, confirming earlier studies and suggesting that the Mg/Ca ratio of seawater determines skeletal mineralogy at the time that carbonate skeletons first evolve in a clade. [. . .]
(2) The major groups of small shelly fossils appear early; five appear by 540-538 Ma, and all but one appear by 534-532 Ma.
(3) By the middle of the Nemakit-Daldynian (534-532 Ma), nearly half of the total number of small shelly fossil genera recorded in our data set had appeared, and by the end of the Nemakit-Daldynian, nearly three-quarters had appeared, suggesting that diversification of these animals occurred throughout the Nemakit-Daldynian, rather than being concentrated at the end of that time. [. . .]
(4) Three pulses in fossil first appearances, the smallest in the early Nemakit-Daldynian , ca. 540-538 Ma, the largest in the middle Nemakit-Daldynian, ca. 534-530 Ma, and the third in the Tommotian, ca. 524-522 Ma, may reflect peaks in small shelly fossil diversification, but could also reflect the influence of local or global preservational biases."

The pattern reported for the small shelly fossils is mirrored in the other animals studied. The above description is generic: there are three pulses of appearance of skeletal animals: a small one at the base of the Cambrian, the largest in the middle of the Nemakit-Daldynian and an intermediate pulse in the Tommotian. Prior to the Cambrian, the seawater is aragonitic; during the Nemakit-Daldynian it is described as aragonite-calcite transition; and in the Tommotian the seawater is calcitic. There is thus an ecological story to accompany the fossil appearance story: the big issue is whether the environmental change drives evolution or whether it constrains evolution or whether it limits the ecological options for animals to feed and breed. The authors recognise that their paper provides a foundation for such discussion to take place:

"An explanation for the processes responsible for the radiation of animals, and of whether the radiation was a consequence or a cause of associated geochemical changes, requires a thorough understanding of the pattern of that radiation, to which this paper contributes."

However, the authors go much further than this in their conclusions. They consider that Darwin's appeal to the imperfection to the fossil record has "turned out to be closer to the truth". In their judgment, the big puzzles are resolved:

"The problem of missing fossil ancestors was solved by the discovery of the Precambrian fossil record, the problem that nearly all the animal phyla appear in the Lower Cambrian with no evidence of intermediate taxa was solved by the recognition that most Lower Cambrian fossils represent stem-groups of living phyla, and the problem of the explosive diversification of animals at the start of the Tommotian was solved by improved correlation and radiometric dating of Lower Cambrian sequences - to which we contribute here - showing that this diversification was drawn out over more than 20 m.y."

It should be obvious that the problem of the early origin of the phyla is not solved by saying that the earliest Cambrian fossils are stem-group rather than crown-group fossils. The challenge to Darwinism posed by the abrupt origins of body plans is undiminished by this fresh analysis. Furthermore, saying that the diversification of animals was drawn out over 20 Ma may reduce the tension for some lineages, but there are still plenty of others where the diversification is inconsistent with Darwinian gradualism (as recently discussed for the echinoderms).

The authors appear to be too eager to sweep away the "Cambrian Explosion" challenge to Darwinism. They might be advised to refer to Meyer, et al. (2006): The Cambrian Explosion: Biology's Big Bang. They may wish also to refer to the work of Thomas Kuhn, who showed how easy it is for scientists to get in a rut and never subject their own presuppositions to critical scrutiny. This has been a real snare for Darwinists who have become experts at slotting every data element into their all-embracing theory. The remedy is to promote multiple working hypotheses. This allows one's own presuppositions to be challenged more easily - and this is healthy for science. The alternative hypothesis this blog has been exploring is that the fossil record is perfectly capable of an ecological perspective. It is there in the Cambrian Explosion data: as soon as environments were capable of being occupied by marine animals, they were colonised. The animals were not suited to aragonite seas, so they are absent from the Ediacaran. But as soon as calcitic seas became widespread, these animals were everywhere. For more on this, with further links, go here.

The earliest Cambrian record of animals and ocean geochemical change
Adam C. Maloof, Susannah M. Porter, John L. Moore, Frank O. Dudas, Samuel A. Bowring, John A. Higgins, David A. Fike, and Michael P. Eddy
Geological Society of America Bulletin, November 2010, v. 122, p. 1731-1774 | doi:10.1130/B30346.1

Abstract: The Cambrian diversification of animals was long thought to have begun with an explosive phase at the start of the Tommotian Age. Recent stratigraphic discoveries, however, suggest that many taxa appeared in the older Nemakit-Daldynian Age, and that the diversification was more gradual. [. . .] The time line suggests that the diversification of skeletal animals began early in the Nemakit-Daldynian, with much of the diversity appearing by the middle of the age. Fossil first appearances occurred in three pulses, with a small pulse in the earliest Nemakit-Daldynian (ca. 540-538 Ma), a larger pulse in the mid- to late Nemakit-Daldynian (ca. 534-530 Ma), and a moderate pulse in the Tommotian (ca. 524-522 Ma). These pulses are associated with rapid reorganizations of the carbon cycle, and are superimposed on long-term increases in sea level and the hydrothermal flux of Sr.

by Denyse O'Leary
ARN correspondent

Molecular biologist Douglas Axe, whose specialty is proteins, has published TheLimits of Complex Adaptation: An Analysis Based on a Simple Model of Structured Bacterial Populations in BIO-Complexity, assessing whether current standard models of evolution are plausible.

A friend writes to explain,

This is a very important paper. It takes on a major problem in population genetics, a problem that has provoked a number of recent papers from our opponents, precisely because they know this issue must be solved before neo-Darwinism can work on any level except the trivial.

Warning: heavy sailing ahead, but the introductory section that challenges Lynch and Abegg is worth reading carefully.

The take home message: gene duplication and recruitment as a model for the evolution of new genes is very limited. It works only if very few changes are required to reach a new selectable function. If the duplicated gene has a slightly negative fitness cost, the maximum number of mutations (in addition to the duplication itself) that a new innovation in a bacterial population can require is two or fewer. If the duplication is cost-free the number of mutations jumps to six or fewer.

Ann Gauger at the Biologic Institute draws attention to this paper as well:

Evolutionary Algorithms: Are We There Yet?

Yes, heavy sailing - in more senses than one, as trolls armed with their iron rice bowls pile on. Author Axe takes a relaxed view of the smoke, mirrors, and noise:

Some people are bothered by the craziness that surrounds the Darwin-v-Design controversy, but I take a more relaxed view. Don’t get me wrong. If I thought there were nothing but craziness, I’d be as frustrated as anyone. But serious science is being done on both sides of the debate, and that should give us confidence that a truer picture of biology will become visible as the smoke clears.

Gauger continues:

In the recent past, several papers have been published that claim to demonstrate that biological evolution can readily produce new genetic information, using as their evidence the ability of various evolutionary algorithms to find a specific target. This is a rather large claim.

It has thus fallen to others in the scientific or engineering community to evaluate these published claims. How well do these algorithms model biology? How exactly was the work done? Do the results make sense? Are there unexamined variables that might affect the interpretation of results? Are there hidden sources of bias? Are the conclusions justified or do they go beyond the scope of what has been shown?

A new paper by Montañez et al. [1], just published in the journal BIO-Complexity, answers some of these questions for the evolutionary algorithm ev [2], one of the computer programs proposed to simulate biological evolution. As perhaps should be no surprise, the authors found that ev uses sources of active information (meaning information added to the search to improve its chances of success compared to a blind search) to help it find its target. Indeed, the algorithm is predisposed toward success because information about the search is built into its very structure.

These same authors have previously reported on the hidden sources of information that allowed another evolutionary algorithm, AVIDA [3-5], to find its target. Once again, active information introduced by the structure of the algorithm was what allowed it to be successful.
These results confirm that there is no free lunch for evolutionary algorithms. Active information is needed to guide any search that does better than a random walk.

Abstract of Douglas Axe’s paper:

To explain life's current level of complexity, we must first explain genetic innovation. Recognition of this fact has generated interest in the evolutionary feasibility of complex adaptations--adaptations requiring multiple mutations, with all intermediates being non-adaptive. Intuitively, one expects the waiting time for arrival and fixation of these adaptations to have exponential dependence on d, the number of specific base changes they require. Counter to this expectation, Lynch and Abegg have recently concluded that in the case of selectively neutral intermediates, the waiting time becomes independent of d as d becomes large. Here, I confirm the intuitive expectation by showing where the analysis of Lynch and Abegg erred and by developing new treatments of the two cases of complex adaptation--the case where intermediates are selectively maladaptive and the case where they are selectively neutral. In particular, I use an explicit model of a structured bacterial population, similar to the island model of Maruyama and Kimura, to examine the limits on complex adaptations during the evolution of paralogous genes--genes related by duplication of an ancestral gene. Although substantial functional innovation is thought to be possible within paralogous families, the tight limits on the value of d found here (d = 2 for the maladaptive case, and d = 6 for the neutral case) mean that the mutational jumps in this process cannot have been very large. Whether the functional divergence commonly attributed to paralogs is feasible within such tight limits is far from certain, judging by various experimental attempts to interconvert the functions of supposed paralogs. This study provides a mathematical framework for interpreting experiments of that kind, more of which will needed before the limits to functional divergence become clear.

A note about the journal BIO-Complexity:

BIO-Complexity BIO-Complexity is a peer-reviewed scientific journal with a unique goal. It aims to be the leading forum for testing the scientific merit of the claim that intelligent design (ID) is a credible explanation for life. Because questions having to do with the role and origin of information in living systems are at the heart of the scientific controversy over ID, these topics—viewed from all angles and perspectives—are central to the journal's scope.

To achieve its aim, BIO-Complexity is founded on the principle of critical exchange that makes science work. Specifically, the journal enlists editors and reviewers with scientific expertise in relevant fields who hold a wide range of views on the merit of ID, but who agree on the importance of science for resolving controversies of this kind. Our editors use expert peer review, guided by their own judgement, to decide whether submitted work merits consideration and critique. BIO-Complexity aims not merely to publish work that meets this standard, but also to provide expert critical commentary on it.

Apparently, there are no vacancies for trolls in the foreseeable future.

Denyse O'Leary is co-author of The Spiritual Brain.

Colorado Springs, CO - December 21, 2010

Access Research Network has just released its annual "Top 10 Darwin and Design Science Stories" for 2010.

Gaining top honors on the list was new research that revealed the optimal design of the human eye. Physicists from the Israel Institute of Technology have created a light-guiding model of the retina, which reveals that the glial (or Muller) cells provide low-scattering passage of light from the retinal surface to the photoreceptor cells, thus acting as optical fibers. Researchers concluded "The fundamental features of the array of glial cells are revealed as an optimal structure designed for preserving the acuity of images in the human retina. It plays a crucial role in vision quality, in humans and in other species." These findings open up potentially fruitful areas for biomimetics research and might find applications in more successful eye transplants and better camera designs.

The gold rush toward biomimetics research (human designs mimicking biological designs) was another top story this year. According to Dennis Wagner, ARN Executive Director "Dozens of articles appeared in the 2010 scientific literature reporting how scientists are learning how to 'reverse engineer' living systems." Examples include: 1) Caltech scientists who are studying jellyfish in order to build a better aquatic pump; 2) German engineers who are building a robotic arm inspired by the design of the elephant trunk; 3) a European team that is building a robotic arm with inspiration from a octopus's limb; 4) swim suits and ship hulls that are being patterned after shark skin; 5) students at the University of Texas, Dallas, that are trying to harness the chemical sensing capability of bacteria to build synthetic sensors for toxins; 6) researchers at the University of Queensland who are inventing navigation systems that can perform complex maneuvers by imitating the optical flow of honeybee eyes; and 7) researchers that are pursuing new lightweight and high performance materials based on a new spider species found in Madagascar that spins silk twice as strong and twice as elastic as any previously studied. This "toughest biomaterial ever seen" is 10 times stronger than Kevlar. Wagner observed, "Many of these research articles seem to miss the rather obvious point that in order to reverse engineer a system, it had to be engineered in the first place."

An online version of the ARN Top 10 Darwin and Design stories for 2010 with hyperlinks to original news sources can be found at www.arn.org/top10.

The NY Times reports that...In 2007, C. Martin Gaskell, an astronomer at the University of Nebraska, was a leading candidate for a job running an observatory at the University of Kentucky. But then somebody did what one does nowadays: an Internet search.

That search turned up evidence of Dr. Gaskell’s evangelical Christian faith.

The University of Kentucky hired someone else. And Dr. Gaskell sued the institution.

Whether his faith cost him the job and whether certain religious beliefs may legally render people unfit for certain jobs are among the questions raised by the case, Gaskell v. University of Kentucky.

More...

NASA Science News for Dec. 17, 2010

Northern winter is beginning in a special way. On Dec. 21st, the winter solstice, a lunar eclipse will be visible across all of North America.

The luster will be a bit "off" on Dec. 21st, the first day of northern winter, when the full Moon passes almost dead-center through Earth's shadow. For 72 minutes of eerie totality, an amber light will play across the snows of North America, throwing landscapes into an unusual state of ruddy shadow.

The eclipse begins on Tuesday morning, Dec. 21st, at 1:33 am EST (Monday, Dec. 20th, at 10:33 pm PST). At that time, Earth's shadow will appear as a dark-red bite at the edge of the lunar disk. It takes about an hour for the "bite" to expand and swallow the entire Moon. Totality commences at 02:41 am EST (11:41 pm PST) and lasts for 72 minutes.

If you're planning to dash out for only one quick look -? it is December, after all -? choose this moment: 03:17 am EST (17 minutes past midnight PST). That's when the Moon will be in deepest shadow, displaying the most fantastic shades of coppery red.

FULL STORY here. And here's the lunar eclipse photo gallery.

Entertain children the old-fashioned way. Don't buy them something. Show them a wonder that belongs to everyone. Then give the money to children's education in developing countries.

by Denyse O'Leary
ARN correspondent

Some have suggested that intelligent design theorists should consider Darwin's much-neglected co-theorist, Alfred Russel Wallace (January 8, 1823-November 7, 1913), an inspiration. Some seem to be taking up the challenge.

Wallace came up with the same "survival of the fittest" idea as Darwin. But - because he found order, meaning, and purpose in the universe - Wallace was not a racist and did not claim that Darwinism was the best idea has ever had, as best-selling authors do today (because it explains the history of life, supposedly).

A key change in the intelligent design controversy in recent years is this: Just what Darwinism really does is slowly but surely becoming a subject of rational enquiry, rather than tax-funded, court-ordered worship.

A friend wrote recently to say,

On Nov. 7, 1913, Alfred Russel Wallace died. Once again, we didn't pay tribute to him in our blogs. I usually wait one day, read the newspapers and magazines, and then post something to remember this date and call attention to the fact that Wallace should also be remembered.

Ah yes, do pay tribute - as long as it is not the ridiculous and appalling hagiography that surrounds Darwin, such that he, his theory, and his tax-supported followers are immune from rational examination.

For the record, Wallace is not a liberator equivalent to Abraham Lincoln, or should it anything like this be said of him:

Darwin revolutionised the biology of his day; he fashioned a new concept of humankind; he challenged basic philosophical and religious ideas about the nature and meaning of life; so profound was his insight that his thought remains relevant to contemporary biology. These surpassing achievements brought a “revolution” equal in importance to the Copernican revolution. Smitten with reverence, my eye falls on the dust jacket to contemplate the photo of the dignified aged Darwin: yes, he looks like a prophet!

Satirical but just. A Wallace admirer would evade this nonsense not because Wallace wasn't a great biologist, but precisely because he was. He deserves a better remembrance than to focus neuroses, as Darwin does, for people who would really be happier swinging from the trees.

My friend advises that a small, old biographical booklet on Wallace can be downloaded free here. He reminds me that this month is the centennial of Wallace's book The World of Life, wherein he lays out his own approach to evolution. Wallace scholar Michael Flannery provides an introduction. Flannery is also shortly to publish a new biography of Wallace with Discovery Institute Press, accompanied by a Web site explaining his intelligent evolution approach. The guardians of the Wallace cult don't like it, and promptly get everything wrong But what would one expect? Science history is too important to be left to cultists.

Also just up at The Post-Darwinist:

Alfred Russel Wallace comes in for some long
overdue recognition

Darwinian atheist Michael Ruse a "practicing Anglican"?

Book Santa will keep for himself: The Nature of nature

Mike Behe replies to detractor Jerry Coyne ...

Neanderthals are people too, it turns out

It's been a while since I have heard from the Sky Is Falling department

Tsk tsk design language: Watch out for those lawyers

Denyse O'Leary is co-author of The Spiritual Brain.

Some have argued that echinoderm diversity is an Ordovician phenomenon: linked to the Great Ordovician Diversification. Others make the case for the radiation to have initiated earlier. All seem to be agreed that the origin of echinoderms is shrouded in uncertainty. One major problem is that the relevant fossils are unfamiliar and often poorly preserved and there are often doubts about their classification. However, in June 2010, research was reported dealing with Middle Cambrian echinoderms from Spain.

"The new Spanish data suggest that a number of the clades involved in [the Great Ordovician] diversification (such as sucocystid cinctans, cothurnocystid stylophorans, ctenocystoids, and isorophid edrioasteroids) appeared significantly earlier in Gondwanan settings than previously thought. This shows that, even by the earliest middle Cambrian, a variety of novel body plans and ecological strategies already existed among echinoderms, pushing back the timing of important divergences into the lower Cambrian."

A Middle Cambrian echinoid - a stromatocystitid edrioasteroid (source here)

The remarkable aspect of this research is the extent of diversification reported. There are eight different body plans that indicate the animals occupied very different ecological niches. This is the ecological interpretation of the fossil record noted in previous blogs.

"There are low to medium suspension feeders (such as gogiids, lichenoidids, or isorophid edrioasteroids) that lived permanently attached; others are free-living forms, such as cinctans, stylophorans, and "eocystitids". Both gogiids and isorophids were commonly attached to skeletal debris. Previous lichenoidids known rested on the substrate, but the new specimens from Spain were also attached to skeletal debris. Cinctans and stylophorans rested on the seafloor and captured particles from the water-sediment interface."

Whatever else is understood from these data, diversification must have been earlier than previously thought. This puts the spotlight on the Early Cambrian - not just providing us with the Cambrian Explosion of animal phyla, but also the emergence of a diversity of ecosystems and the radiation of animal groups.

"Because many of these taxa appear close to the beginning of the middle Cambrian, it seems likely that their origins must be placed in the early Cambrian."

It should be remembered that the sea urchin, an echinoderm, is one of the animals whose genomes has been sequenced. Two of these genes, pax and BOULE, have been the subject of previous comment (here). Those involved with the sequencing expressed surprise at finding such sophistication, for it was realised that much of the animals genetic makeup is remarkably similar to that possessed by humans. This early appearance of genetic complexity is a major aspect of the Cambrian Explosion - for these animals were not simple or primitive in their genetic makeup. Such a flowering of biological information is inconsistent with the gradualism inherent in darwinian mechanisms.

"Any snorkeler who has ever marvelled at the spherical, almost otherworldly, symmetry of the sea urchin will be amazed to learn that this organism, so different in habitat and body plan from ourselves, actually shares a substantial number of the same genes and pathways," said Francis Collins, director of the National Human Genome Research Institute (NHGRI) which helped fund the project.
"It turns out that the sea urchin is very much like us," said George Weinstock, the co- director of the HGSC. "You wouldn't think it to look at it. But it's closer to us than a fly," he said. (Source here)

Middle Cambrian echinoderms from north Spain show echinoderms diversified earlier in Gondwana
Samuel Zamora
Geology, June 2010, 38(6), 507-510 | doi:10.1130/G30657.1

Abstract: New fossil discoveries in the middle Cambrian of Spain have considerably expanded our knowledge of the temporal and spatial distribution of some major clades of echinoderms including sucocystid cinctans, isorophid edrioasteroids, cothurnocystid stylophorans, ctenocystoids, and a new group of blastozoans ("eocystitids"). Because many of these taxa appear close to the beginning of the middle Cambrian, it seems likely that their origins must be placed in the early Cambrian. These results, based on articulated specimens provided from Echinoderm Lagerstatten, agree with the hidden diversity provided from isolated ossicles from other Gondwanan areas.

Casey Luskin wrote an article for the Christian Science Monitor on the Louisiana textbook decision. Luskin writes that...

Critical inquiry and freedom for credible dissent are vital to good science. Sadly, when it comes to biology textbooks, American high school students are learning that stubborn groupthink can suppress responsible debate.

In recent weeks, the media have been buzzing over a decision by the Louisiana State Board of Elementary and Secondary Education to adopt biology textbooks. A Fox News summary read "Louisiana committee rejects calls to include debate over creationism in state-approved biology textbooks...." There was one problem with the story. Leading critics of evolution in Louisiana were not asking that public schools debate creationism, or even that they teach intelligent design. Rather, they wanted schools to simply teach the scientific debate over Darwinian evolution.

More...

by Denyse O'Leary
ARN correspondent

Mike Behe's reply (excerpt):

Yes, complex gain-of-FCT events would not be expected to occur, but simple GOF's would. Yet they didn't show up.

Professor Coyne then proceeds to put words in my mouth:

What [Be]he's saying is this: "Yes, gain of FCTs could, and likely is, more important in nature than seen in these short-term experiments. But my conclusions are limited to these types of short-term lab studies."

No, that is not what I was saying at all. I was saying that, no matter what causes gain-of-FCT events to sporadically arise in nature (and I of course think the more complex ones likely resulted from deliberate intelligent design), short-term Darwinian evolution will be dominated by loss-of-FCT, which is itself an important, basic fact about the tempo of evolution.
Above I quoted Coyne talking about "complex FCTs, which take time to build or acquire from a rare horizontal transmission event." Yet cells aren't going to sit around twiddling their thumbs until that rare event shows up. Any mutation which confers an advantage at any time will be selected, and the large majority of those in the short term will be LOF. Ironically, Coyne seems to underestimate the power of natural selection, which "is daily and hourly scrutinising, throughout the world, every variation, even the slightest...." A process which scrutinizes life "daily and hourly," as Darwin wrote, isn't going to wait around for some rare event.

Denyse O'Leary is co-author of The Spiritual Brain.

by Denyse O'Leary
ARN correspondent

"This study reports evidence consistent with the 'deliberate fraud' hypothesis. The results suggest that papers retracted because of data fabrication or falsification represent a calculated effort to deceive.":

Med Ethics doi:10.1136/jme.2010.038125

Research ethics

Retractions in the scientific literature: do authors deliberately commit research fraud?

R Grant Steen
Correspondence to
R Grant Steen, Medical Communications Consultants LLC, 103 Van Doren Place, Chapel Hill, NC 27517, USA; g_steen_medicc@yahoo.com
Received 31 May 2010
Revised 29 July 2010
Accepted 13 August 2010
Published Online First 15 November 2010
Abstract
Background Papers retracted for fraud (data fabrication or data falsification) may represent a deliberate effort to deceive, a motivation fundamentally different from papers retracted for error. It is hypothesised that fraudulent authors target journals with a high impact f actor (IF), have other fraudulent publications, diffuse responsibility across many co-authors, delay retracting fraudulent papers and publish from countries with a weak research infrastructure.

Methods All 788 English language research papers retracted from the PubMed database between 2000 and 2010 were evaluated. Data pertinent to each retracted paper were abstracted from the paper and the reasons for retraction were derived from the retraction notice and dichoto mised as fraud or error. Data for each retracted article were entered in an Excel spreadsheet for analysis.

Results Journal IF was higher for fraudulent papers (p<0.001). Roughly 53% of fraudulent papers were written by a first author who had written other retracted papers (‘repeat offender’), whereas only 18% of erroneous papers were written by a repeat offender (?=88.40 ; p<0.0001). Fraudulent papers had more authors (p<0.001) and were retracted more slowly than erroneous papers (p<0.005). Surprisingly, there was significantly more fraud than error among retracted papers from the USA (?2=8.71; p<0.05) compared with the rest of the world.

Conclusions This study reports evidence consistent with the ‘deliberate fraud’ hypothesis. The results suggest that papers retracted because of data fabrication or falsification represent a calculated effort to deceive. It is inferred that such behaviour is neither naï ve, feckless nor inadvertent.

For comments go here "The highest number of retracted papers were written by US first authors (260), accounting for a third of the total. One in three of these was attributed to fraud.", or here (An excellent example of either crappy science reporting or crappy science ...), for the view that it's all a bum rap.

One site also offers a number of articles on the shortcomings of peer review. Also an article on self-plagiarism and one on self-plagiarism and bogus authorship.

Self-plagiarism? If I plagiarize myself, can I sue myself?

Self-Plagiarist dies of his pains,
When "Been done!" the reviewer complains.
He was suing himself
In a courtroom in Guelph,
And his spectre now sues his remains.

Denyse O'Leary is co-author of The Spiritual Brain.

by Denyse O'Leary
ARN correspondent

My Salvo 15 Deprogram column:

LUCY SPEAKS
Evolutionary Psychology Is Now Taking Your Questions

When Britain's Guardian newspaper first introduced its "evolutionary" agony aunt (advice columnist in America) in 2009 - to honor 150 years of the culture birthed with Charles Darwin's 1859 book, On the Origin of Species - I thought, "Aha! a send-up, to be sure." I was wrong, but in fairness, when the evolutionary psychologist speaks, even an expert can't always tell.

No spoof. The Guardian burbled proudly about Carole Jahme, author of Beauty and the Beasts: Woman, Ape and Evolution and winner of the Wellcome Trust Award for Communication of Science to the Public. For the 2009 Darwin bicentennial celebrations, Jahme, who holds an M.A. in evolutionary psychology, put together a comedy show titled Carole Jahme is Sexually Selected, which was described as a combination of Charles Darwin and Charlie Chaplin.

The Guardian touts her column as "shin[ing] the cold light of evolutionary psychology" on readers' problems, thus apparently offering welcome relief from the "Aw, just dump the dweeb!" froth churned out by glossier rags and mags.

For more, go here.

And treat yourself or a friend to a year-long Salvo of light-hearted fun at the expense of publicly venerated nonsense.

Denyse O'Leary is co-author of The Spiritual Brain.

At Slate, Daniel Engber offers another slam at peer review:

When journal editors are asked about these ideas, they often quote Winston Churchill's line, "Democracy is the worst form of government except all those other forms that have been tried from time to time." Or rather, they quote other journal editors quoting that line. But it's a poor analogy, since few alternatives to peer review have been tried in modern times. And democracy isn't really a good description of peer review, either. Sure, peer review allows scientists to participate in a system of self-governance. But wouldn't BMJ's policy of open review or Ginsparg's proposal for Web-published preprints be far more democratic?

So far, though, the Churchill quoters are winning.

You know, "The worst system , except for all the others." The trouble is, any system can exhaust the benefits for which it was brought in- in this case, to cope with the flood of post-World War II science efforts. In my own view, it has become the same sort of drag on fresh thinking as reliance on Aristotle was in the early modern period of science.

If the object is to do good science while pleasing all possible reviewers, and the gist of the paper is an idea that disconfirms their theories, one may have to downplay findings, quit the field, or go nuts. Michael Behe is a rare example of someone who stood up to all the garbage, just to make a simple point or two about the shortcomings of Darwin's Rice Bowl.

Other peer review stories:

Peer review: How much more believable than fortunetelling?

"Peer review, mere review, and smear review"

"Peer review: Life, death, and the British Medical Journal"

Science: A year-end wad of fraud, falsified data, and other award-winning tenure strategies ...

Peer review: What if your peers would have to be otherconspiracy theorists? (No, really!)

Peer review: Gold standard or gold in "them thar hills"

Casey Luskin writes ENV...Martin Gaskell is an astronomer who is originally from the United Kingdom. He came to the U.S. in 1975 and later received his M.S. and Ph.D. at the University of California at Santa Cruz. He's not a creationist. As we'll see below, he's generally a theistic evolutionist, who has at times expressed minor criticisms of some aspects of evolution (he accepts common ancestry) and an openness to the possibility of intelligent design. In 2007, Gaskell was on the faculty at the University of Nebraska, Lincoln, where he taught in the Department of Physics and Astronomy. At that time, he applied for a job at the University of Kentucky (UK), hoping to serve as the founding director of a newly planned observatory. But the UK didn't hire Gaskell. Instead they hired Timothy Knauer, who was considerably less experienced. Why? The hiring search committee at UK confused intelligent design (ID) with theistic evolution, and both with creationism, ending up with Gaskell filing a religious discrimination lawsuit against UK. His case shows that if academia merely thinks you're an ID-sympathizer - regardless of whether you actually are - then you're a "creationist" who should have no role in public outreach at the university.

More...

by Denyse O'Leary
ARN correspondent

Apparently, Jerry Coyne is now attacking me, re Behe's recent paper. To judge from his blog post's title, he has me confused with Discovery Institute.*

(Behe's paper is available for free download here).
.
Dr. Coyne claims that Behe's findings apply only to artificial selection in the lab. But, at the feet of the great Richard Dawkins, I learned that artificial selection like human breeding of dogs, has proved Behe both wrong and ridiculous, in Edge of Evolution. That is precisely because dog breeding is equivalent to the process that applies throughout nature:

Don’t evade the point by protesting that dog breeding is a form of intelligent design. It is (kind of), but Behe, having lost the argument over irreducible complexity, is now in his desperation making a completely different claim: that mutations are too rare to permit significant evolutionary change anyway. From Newfies to Yorkies, from Weimaraners to water spaniels, from Dalmatians to dachshunds, as I incredulously close this book I seem to hear mocking barks and deep, baying howls of derision from 500 breeds of dogs — every one descended from a timber wolf within a time frame so short as to seem, by geological standards, instantaneous.

All you have to do, it seems, is leave out intelligent design.

Dawkins said this in the Bible, and all the wise nodded in assent.

Well, either artificial selection is relevant or it isn't. Maybe Coyne and Dawkins should talk more.

*We share some initials, it's true. My middle name is Ileen. The confusion is inevitable.

Also just up at The Post-Darwinist:

Could Darwinists be running low on insults?

But I really DO think that Christian Darwinism is an oxymoron

You'd rather watch this than passing trains

Saturday morning coffee break: Frosty the Snowman was not designed, he evolved

Listening: Michael Behe crosses the (not!) warm little Pond

f you are a Darwinist, can you be a Christian if people just say so ... ?

From the quote mine: Themisunderestimated virtues of skepticism

Denyse O'Leary is co-author of The Spiritual Brain.

by Denyse O'Leary
ARN correspondent

Mike Behe,
widely hated author of Edge of Evolution has been on the road recently, in Britain.

Behe's most recent heresy has been to detail what Darwinism can and can’t do, as shown in experiments and evidence. For some reason, that man has a problem with rehabilitating magic and calling it Darwinian evolution - but that is just what heretics are like.

Apparently, he got quite a bit of response, and not only from Darwin’s rice bowls. Here’s a radio program with a British Christian Darwinist, Keith Fox. Go here for the mp3 podcast and here for Itunes.

The skinny:

It was a shock to people of the nineteenth century when they discovered, from observations science had made, that many features of the biological world could be ascribed to the elegant principle of natural selection. - Michael Behe

It is a shock to us in the twentieth century to discover, from observations science has made, that the fundamental mechanisms of life cannot be ascribed to natural selection, and therefore were designed. But we must deal with our shock as best we can and go on. - Michael Behe

Read more here.

Denyse O'Leary is co-author of The Spiritual Brain.

Until this year, the Bryozoa were missing from the list of Cambrian organisms. Although some had been previously reported, critical scrutiny showed that they were misidentified and that the oldest known bryozoans came from Lower Ordovician strata. This year, however, Upper Cambrian bryozoans were reported from the lower Tinu Formation, southern Mexico. They were said to be about 8 Ma years older than the oldest Ordovician fossils. This means that Cambrian strata can be said to record examples of all the skeletalized metazoan phyla.

"One mineralized group, the phylum Bryozoa, seems to have "missed" the Cambrian radiation. [. . .] As discussed below, Late Cambrian bryozoans are now known, and have features that suggest they lie near the base of the bryozoan lineage."

"Bryozoa", from Ernst Haeckel's Kunstformen der Natur, 1904 (source here)

In view of the ecological perspective this blog has been giving to the appearance of organisms in the fossil record (see here), it is worth highlighting the ecological significance of bryozoans. This is brought out in the following paragraph:

"Bryozoans are an important Paleozoic-Holocene phylum in substrate stabilization, as a food source and major filter-feeding group, as rock formers, and as a component of a new Late Ordovician habitat - animal-constructed reefs. Late Ordovician bryozoan-coral-stromatoporoid reefs were colonized by high-diversity faunas. These reefs replaced earlier, microbially formed, thrombolite reefs. The Tinu Formation shows that Bryozoa, as all other mineralized metazoan phyla, had a Cambrian origin, although Bryozoa formed only small Early Ordovician reefs."

The Cambrian, then was a remarkable period of Earth history. In the Precambrian, we have only soft-bodied organisms. At the end of the Cambrian, we have all the skeletalized metazoan phyla and much more besides. Subsequent periods of Earth history may have had more dramatic radiations at the Order, Class or Family level, but there were no further bauplan innovations affecting skeletalized metazoan organisms.

This phenomenon has long been troubling for the Darwinian paradigm. The branching pattern of speciation endorsed by Darwin and his followers implies that Family, Class, Order and Phylum categories emerge as later stage developments of the evolutionary process. What we see in the fossil record, however, is the opposite of this. We start with discontinuity of body plans, followed by diversification - as variation around a theme. Darwinists have never confronted their theory with the facts - they exhibit all the characteristics of Kuhnian 'normal science' that will force-fit anomalous data to theory. For more on this and the 'inverted cone of diversity', go here.

Cambrian origin of all skeletalized metazoan phyla - Discovery of Earth's oldest bryozoans (Upper Cambrian, southern Mexico)
Ed Landing, Adam English and John D. Keppie
Geology, June 2010, 38(6), 547-550 | doi:10.1130/G30870.1

Abstract: Exquisite Pywackia baileyi Landing n. gen. and sp. specimens from the lower Tinu Formation, southern Mexico, extend the bryozoan record into the Upper Cambrian. They are ~8 m.y. older than the purported oldest bryozoans from South China, and show that all skeletalized metazoan phyla appeared in the Cambrian. The new form differs from similar, twig-like cryptostomes by its shallow autozooecia and an elongate axial zooid, which may be homologous to the stolon in nonmineralized ctenostomes. It may morphologically resemble mineralized stem group bryozoans that retained a stolon-like individual, although an ability to bud was acquired by the feeding individuals (autozooids). The latest Cambrian origin of bryozoans, several mollusk classes (polyplacophorans, cephalopods), and euconodonts was a major evolutionary development and can be considered the onset of the Ordovician radiation of more complex marine communities.

On December 2, 2010 NASA staged a big press release to announce the discovery of an arsenic-based form of DNA that will impact the search for evidence of extraterrestrial life. This week Slate dismissed the issue as shoddy science.

Unlike Darwin's bicentennial, here is one anniversary that is certainly worth celebrating. Unlike Darwin's rock pile, here is one example of how the science of today is building on the solidity of yesteryear's durable substructure. Anti-evolutionists are not anti-science. But they are opposed to the beligerence of those who contumaciously refuse to accept the broader implications of science's beautiful procession towards the truth.

Students of the Cambrian Explosion have had much to think about this year. In this blog, and others to follow, several of these will be featured. We start with Nectocaris, one of the 'weird wonders' of Stephen Jay Gould in Wonderful Life. There have been many attempts to locate it within the traditional taxonomic framework. Some have placed it in the arthropods and others have considered it a chordate. However, research published earlier this year, based on 91 specimens (rather than one), has concluded that the animal is a mollusc.

The (reconstructed) ancient squid hunted using its two long tentacles (Source here)

Martin Smith and Jean-Bernard Caron have suggested that Nectocaris displays characters that put it into a relationship with cephalopods. They point to paired camera-type eyes, flexible tentacles and jet propulsion via a 'nozzle'. The reconstructed animal has the appearance of a squid but with two rather than eight or ten tentacles. They suggest that the animal is a stem-group rather than a crown-group cephalopod. It lacks features they consider to be more advanced: there is no shell, only two tentacles and no obvious beak or radula (although the mouthparts are poorly preserved). Their analysis has been accepted by most commentators. The relevance to the Cambrian Explosion is that, before now, the earliest fossil remains of cephalopods are Late Cambrian. Since the studied samples all come from the Middle Cambrian Burgess Shale Formation, Nectocaris "extends the cephalopods' fossil record by over 30 million years".

"The findings make the ancestors of modern squid and octopuses at least 30 million years older. Evolutionary biologist Martin Smith, the main author of the study, told PA news agency that the findings bring cephalopods much closer to the first appearance of complex animals. "We go from very simple pre-Cambrian life-forms to something as complex as a cephalopod in the geological blink of an eye, which illustrates just how quickly evolution can produce complexity," said Mr Smith."

The above quote from Martin Smith illustrates both the significance for the Cambrian Explosion and the conundrum the evidence provides for evolutionary theory. The problem is that everything occurs "in the geological blink of an eye" - whether it be the origins of the phyla with radically different body plans, or whether it be the origins of different classes within a phylum (such as the origin of cephalopods within the mollusca). In a News & Views essay for Nature, Stefan Bengtson provides an insight into these animals.

"To most people, molluscs are rather dull creatures: slugs, snails, clams, mussels and such, at times good for eating but otherwise uninteresting. Yet everyone harbours a fascination for cephalopods, which are also molluscs: the octopus, the chambered nautilus, the cuttlefish and the squid, not least the mythical giant Kraken that Alfred, Lord Tennyson pictured in "ancient, dreamless, uninvaded sleep" in the ocean abyss. Cephalopods are not like other molluscs.
Anything but sluggish, they are capable of instant and rapid movement. Far from being mindless filterers or grazers, they are active predators possessing the most advanced nervous system known among invertebrates. Their brain-to-body ratio exceeds that of most vertebrates (although we have not been smart enough to figure out exactly how smart they are). They are masters of camouflage, changing shape, surface pattern, texture and colour in the blink of an eye - and they do have good eyes. When threatened, they escape by means of a built-in hydro jet that can even send them squirting through the air like little rockets on a tail of water."

At very least, then, if the identification of Nectocaris as a cephalopod is valid, the time available for evolutionary transformation is reduced by 30 Ma. The credibility of gradualist mechanisms, already at breaking point, simply vanishes. It is a cop-out to say that the data "illustrates just how quickly evolution can produce complexity" because it begs the question that evolution can generate complexity at all. Martin Smith's words are the evolutionary biologist's equivalent of the 'god-of-the-gaps' argument. He has no mechanism to explain how it could ever happen, but since evolution is regarded as a 'fact', then evolution must have done it.

It is worth considering whether Nectocaris is primitive or derived. The authors entertain this idea when they write: "Nectocaridids' single pair of tentacles may originate via the fusion of multiple pairs, or represent the primitive state". They also articulate the puzzle of having mineralised ancestors and mineralised descendants - but opt for Nectocaris being primitive because "no obvious precursors" for cephalopods have been found. They resolve their conundrum by postulating that there must have been non-mineralised precursors:

"Given that the highly plastic molluscan secretome has convergently produced similar shell microstructures in unrelated lineages, we suggest that nautiloids evolved from a nonmineralized, coleoid-like ancestor related to the nectocaridids."

Not all are convinced. Christopher Taylor finds reasons for thinking that Nectocaris is not such a primitive animal, but a specialised organism (and that, it should be said, raises even more puzzles for the Darwinian, gradualist paradigm).

"As described in an earlier post, the earliest known stem cephalopods (from the Late Cambrian) possessed shells with large numbers of very tightly packed septa and were unlikely to have been very buoyant. Their generally short conical shape would have been ill-suited for jet-propelled swimming as in modern cephalopods and they were most likely benthic. As other molluscan classes were also ancestrally benthic, it seems unparsimonious that the actively swimming Nectocaris represents the ancestral cephalopod lifestyle.
If Nectocaris is a stem cephalopod (which essentially depends on how strong the siphon is as a supporting apomorphy), then the most likely scenario is that its shell loss and squid-like form is an independent convergence on modern shell-less cephalopods rather than representing the ancestral form for cephalopods as a whole. Nectocaris would not be an ancestor, but a highly specialised side branch of its own."

Primitive soft-bodied cephalopods from the Cambrian
Martin R. Smith and Jean-Bernard Caron
Nature, 465, 469-472, (27 May 2010) | doi:10.1038/nature09068

Abstract: The exquisite preservation of soft-bodied animals in Burgess Shale-type deposits provides important clues into the early evolution of body plans that emerged during the Cambrian explosion. Until now, such deposits have remained silent regarding the early evolution of extant molluscan lineages - in particular the cephalopods. Nautiloids, traditionally considered basal within the cephalopods, are generally depicted as evolving from a creeping Cambrian ancestor whose dorsal shell afforded protection and buoyancy. Although nautiloid-like shells occur from the Late Cambrian onwards, the fossil record provides little constraint on this model, or indeed on the early evolution of cephalopods. Here, we reinterpret the problematic Middle Cambrian animal Nectocaris pteryx as a primitive (that is, stem-group), non-mineralized cephalopod, based on new material from the Burgess Shale. Together with Nectocaris, the problematic Lower Cambrian taxa Petalilium and (probably) Vetustovermis form a distinctive clade, Nectocarididae, characterized by an open axial cavity with paired gills, wide lateral fins, a single pair of long, prehensile tentacles, a pair of non-faceted eyes on short stalks, and a large, flexible anterior funnel. This clade extends the cephalopods' fossil record by over 30 million years, and indicates that primitive cephalopods lacked a mineralized shell, were hyperbenthic, and were presumably carnivorous. The presence of a funnel suggests that jet propulsion evolved in cephalopods before the acquisition of a shell. The explosive diversification of mineralized cephalopods in the Ordovician may have an understated Cambrian 'fuse'.

See also:

Bengtson, S. A little Kraken wakes, Nature, 465, 427-428, (27 May 2010) | doi:10.1038/465427a

Moskvitch, K. Mystery fossil is ancestor of squid, BBC News (27 May 2010)

Taylor, C. Nectocaris: Largely Irrelevant to Cephalopods? Catalogue of Organisms (27 May 2010)

This should be interesting...

Link here...

Casey Lusken, in ENV, gives tribute to a great scientist and ID advocate Dr. Phillip Skell.

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On ID the Future...Dr. Donald L. Ewert continues to explain why the vertebrate adaptive immune system does not use "random" or "chance" processes like Darwinian evolution to generate antibody diversity. Instead, he argues that the immune system is intelligently designed. Listen in as Dr. Ewert shares one of the most interesting stories in science, the generation of antibody diversity.

Link to audio...

As reported on Uncommom Descent...Michael Behe is currently on a speaking tour around the UK (tour website here), organised by the newly founded Centre for ID UK. Last night, the Glasgow lecture was entitled "Darwin or Design - What Does the Science Really Say?" As is to be expected, Behe spoke both articulately and persuasively, developing a powerful cumulative positive case for design based on the nanotechnology which pervades life at the level of the cellular world. Behe is a very gifted speaker, especially when it comes to conveying his scientific ideas and concepts to an audience without a scientific background.

Link to blog...

Online videos of the debate between renowned atheist Christopher Hitchens and intelligent design proponent William Dembski over God's existence were in such high demand Monday that the school behind the event said it had to relocate the content to another server.

Mary Carl Finkelstein, special assignments coordinator at Prestonwood Christian Academy and organizer of the debate, told The Christian Post that over 5,000 viewers accessed the online videos Monday morning, causing the school to search for a different server to better host the videos.

Link to article...

The Baptist Press reports on the debate. Intelligent Design proponent William Dembski and famed atheist Christopher Hitchens disputed the existence of a benevolent God in a recent debate.

Link to article...

The word "proves" may be a stretch, but a cumulative case continues to be built.

As reported in Uncommon Descent, seeing is believing.. Over at Creation.com, Brian Thomas has posted a fascinating article entitled, ATP synthase: majestic molecular machine made by a mastermind. ATP synthase is an enzyme that synthesizes an energy-rich compound, ATP (adenosine triphosphate), which is used by almost every biochemical process in the body. ATP synthase is also the world's tiniest rotary motor, and it operates at near 100% efficiency, which is far greater than that of any man-made motor. In his article, Brian Thomas does an excellent job of describing the workings of this enzyme and of exposing the inadequacies of proposed evolutionary explanations for its origin.

Click HERE to see the article and video...

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As reported in Medical Daily, researchers at the Stanford University School of Medicine, applying a state-of-the-art imaging system to brain-tissue samples from mice, have been able to quickly and accurately locate and count the myriad connections between nerve cells in unprecedented detail, as well as to capture and catalog those connections' surprising variety.

Observed in a new method called array tomography, the brain's overall complexity is almost beyond belief, said Stephen Smith, PhD, professor of molecular and cellular physiology at Stanford University. "One synapse, by itself, is more like a microprocessor - with both memory-storage and information-processing elements - than a mere on/off switch. In fact, one synapse may contain on the order of 1,000 molecular-scale switches. A single human brain has more switches than all the computers and routers and Internet connections on Earth," he said.

"In a human, there are more than 125 trillion synapses just in the cerebral cortex alone," said Smith. That's roughly equal to the number of stars in 1,500 Milky Way galaxies, he noted.

Mark Hartwig, long time ID advocate, commented that "Probably the only thing more complex than this will be Darwinists' explanation of how a mindless process and time produced such stunning structures."

The article...

On the Uncommon Descent web site, Gil Dodgen opines on the Dembski-Hitchens debate in Texas.

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Written by Felipe Aizpun Vines, OIACDI; 2010, ISBN 10-1452800790; Review by Carlos Javier Alonso, University of Navarra, Spain (see original review in Spanish at OIACDI); Translation by Robert Deyes

Evolucionismo y conocimiento racional (Evolution and rational thought) presents a thoroughly comprehensive analysis of both the arguments in favor and against evolution and demonstrates the author's deep understanding of scientific literature published over the last few decades on the subjects of life's origins and the evolution of man. This timely volume deals with the subject matter in extraordinary depth through its coverage of both classical and contemporary viewpoints from the various schools of evolutionary thought. The 622-page text of Evolucionismo y conocimiento racional is divided up into 21 chapters that systematically unpack the following topics: Darwinism, Evolution: fact or theory, materialist prejudices, creationism, fundamentalism, rational thought, science and philosophy, routes of reason, shortcomings of the scientific method, the 'new biology', intelligent design, evolution and creation and the philosophy of life.

Evolucionismo y conocimiento racional stands out as a resource that brings together the core elements of the topics it covers and thus provides an avenue for readers to assess the current state of debate. In this regard Evolucionismo y conocimiento racional can be seen as the 'evolution bible'. Rather than giving the impression of a rapidly assembled collection of facts put together for the sole purpose of disseminating information, the book bears all the hallmarks of a well thought out literary masterpiece. Most notable is the rich collection of arguments through which each of the evolutionary hypotheses are expounded and systematically considered. And yet Evolucionismo y conocimiento racional is not exclusively directed towards specialist readers. On the contrary. In my assessment, it is easily accessible to those who have a basic training in philosophy and science and a firm grasp of the multi-faceted problems surrounding evolutionary reasoning.

Understood in a purely biological context, evolution is not a fact in itself but rather an interpretation of the facts as we find them. To be sure, no scientific specialty can claim to faithfully reconstruct what happened hundreds of thousands let alone millions of years ago. The relevant disciplines only allow us to make conjectures or presumptions regarding the journey that evolution has taken. It therefore follows that evolution carries with it an inherent (not necessarily false) bias and constitutes a hypothesis lacking the empirical support so necessary to establish it as a scientific theory.

Criticisms of the Darwinist paradigm and its neo-Darwinist reformulation are sufficiently convincing, not easily refutable and solidly rigorous. As Felipe Aizpun shows, Darwin's lack of understanding of genetics prevented him from drawing up a mechanism through which evolution could run its course. But the neo-Darwinist revision fares no better. The proposed combination of favorable random mutations preserved by natural selection falls short in every aspect.

The author compellingly asserts that the chance assessment of events exists nowhere other that in the minds eye. There are numerous causal factors that can affect the outcomes of natural processes and there is no way to predict which factors will act to produce a given outcome. The complexity of nature makes such predictions very difficult if not impossible given that causal factors that act in one instance might be absent in others. An appeal to 'chance' is an appeal made from ignorance of what causal factors are at play in the manifestation of a reality that we observe. Only in relation to a partial cause can we talk about chance. For these reasons the Darwinian paradigm, defined in Kuhnian terms, is one that is rife with anomalies and thereby one that is on the verge of a revolutionary crisis. While the alternative offered by Professor Maximo Sandin and biologist Lynn Margulis amongst others still carries with it significant gaps in understanding and points of contention (these are discussed with noteworthy precision and clarity in chapters 17 and 18) it could still unseat the official paradigm in the short term not only because of its more coherent consideration of the facts but also because the causal factors it invokes better explain the phenomenon of evolution.

Evolucionismo y conocimiento racional supplies an accurate analysis of scientific naturalism which at its core reduces all understanding to that which is experimentally demonstrable. Scientific naturalism is a theory that states that only experimental science can provide a valid understanding of reality and that scientific investigation alone meets the needs of human intelligence. In accordance with this doctrine there has been a pinning down that unjustifiably restricts all human understanding to the confines of science. Nevertheless we cannot lose sight of the fact that science is not the only system available to us for acquiring knowledge. Undoubtedly a large part of what we know and what we have achieved has come to us from sources outside the scientific enterprise. The avenues along which man can understand reality are many. Beyond genetic inheritance, traditions and personal experience as well as art, crafts, religion, poetry and philosophy can provide a basis for understanding diverse aspects of our experience. While scientism claims that knowledge of our world is limited to that which is obtainable through experimental science, reducing all objectivity to that which is experimentally acquired blinds us to the fact that the scientific/natural picture is only one branch of the total human experience.

Another matter deserves our attention- the criticism (in my opinion questionable) of Tomist metaphysics and of the evidential force of his five arguments for the existence of God. According to the author such arguments imply the possibility of demonstrating the existence of God deductively. The author displays a partiality towards inferring the existence of God in probabilistic terms in accordance with the abductive line of reasoning put forward by Charles Sanders Pierce. A consideration of God's existence through probability rather than certainty, the latter being in accordance with a deductive mode of reasoning, has important ramifications. For example, a discourse on the foundations of morality on God would only fit into the religious context of revelation and would require from us additional efforts if we were to find an exclusively rational explanation, understood as an unavoidable commitment to action that could elude the subjectivist and relativist trap to which we would be destined.

Regarding this point the author reveals himself to be a partial doubter of the Kantian epistemology and criticism of the Tomist arguments. In his view, the Kantian criticism is made up of two parts that need to be differentiated. On the one hand we are to reflect on the fact that the deductive process for a cosmological argument is inconsistent given that it assumes an identification of the ideal concept of the necessary being with the being of realism even though such a connection is not rationally admissible. On the other hand, Kant concludes equivocally, taken by an arbitrary epistemological limitation, that transcendent ideas are inaccessible to reason. Although accurate the Kantian criticism of the Tomist approach, notes the author, the idea that God is not foreign to our rational state and the Kantian conclusion of unknowability, does not necessarily follow. What needs to be defined is an adequate method of reasoning that takes us to a primary cause and its connection with sensible knowledge.

One has to specifically acknowledge that there is something that is simply erroneous in the statement that knowledge exists exclusively as a function of sensible knowledge. Such a stance implies a rejection of formal abstraction and the separation of diverse aspects of being such as the modes of cognitive access and reality. To negate such an abstraction and separation is to obstruct the pathway towards God, given that we will not be able to access the being of those creatures.

Evolucionismo y conocimiento racional falls firmly within the paradigm of Intelligent Design. Seen from our vantage point, the design inference that comes from the study of living creatures is a completely logical one (one has to be blind not to see this); this is the inference that the latest theories- both theistic and more recently those of intelligent design- have put forward both in philosophical and scientific circles; such theories have generated much animosity amongst Darwinists, with their fundamental assumption of natural selection acting on random mutations. In any case, one has to recognize that all theories categorized under the ID umbrella play on two fields: that which argues strictly on scientific grounds (the work of Behe and Dembski concerning irreducible complexity and specified complexity in addition to their critique of the neodarwinist explanation, are paradigmatic examples of this) and also that which argues on philosophical grounds since they postulate the existence of a Designer as the causal agent that is necessary for the design. Within this perspective, ID theories do not fit strictly into the experimental scientific method and can therefore be considered as non-scientific. Nevertheless this does not mean that they are false since reality is not confined to that which we can observe through experimental science. Rather it means that these theories are at the same time both scientific and philosophical in nature.

In view of these points, Evolucionismo y conocimiento racional is a must-read for those wishing to remain up-to-date with contemporary evolutionary theories and the arguments that support them.

Dr. Carlos Javier Alonso obtained his PhD in philosophy from the University of Navarra in Spain. He also holds a degree in hispanic philology from the University of Leon and is an associate professor at the Instituto de Educacion Secundaria Ordono II in Leon. He is the author of several books on science including El Evolucionismo y Otros Mitos: La Crisis del Paradigma Darwinista (transl. Evolutionism And Other Myths: The Crisis Of The Darwinist Paradigm)

According to reviewer Dora the new online game CellCraft "is one part resource management, one part puzzle, one part strategy, and even one part funny. Oh, and did I mention? It's(*gasp!*)... educational!"

If you are looking for a fun way to teach your kids (or yourself) about the complexity and of the cell give this new online game a try. It can be played at the popular Kongragate website or you can download a copy to your computer from the CellCraft game website.

by Denyse O'Leary
ARN correspondent

My review of Cordelia Fine's new book, Delusions of Gender: How Our Minds, Society, and Neurosexism Create Difference:

The gender wars take no prisoners. In 2005, suggesting that there might indeed be innate differences between men and women derailed the career of Harvard president Larry Summers. He reemerged, years later, as President Obama’s sometime finance guru). Meanwhile, a host of neuroscientists report differences between the brains of men and women that, they say, account for different abilities and career choices.

Psychologist and author Cordelia Fine disagrees with the neuroscientists. In Delusions of Gender: How Our Minds, Society, and Neurosexism Create Difference, she has no time for the "special powers" that pop brain science currently imputes to the female brain, reminding us that such claims were made long before the magnetic resonance imaging machine was invented.

She takes aim at books such as What Could He Be Thinking? where we hear that images of male and female brains were "marriage saving" for author Michael Gurian and his wife, to say nothing of Gurian's Leadership and the Sexes which "links the actual science of male/female brain differences to every aspect of business."

And if that doesn't make you feel like Employee Double X or XY clocking in, what will?

For more, go here.

See also:

Evolutionary psychology: Pink for a girl, blue for a ... girl?

Neuroscience: Philosopher rips "drivel" - pop science media's bread and butter

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

by Denyse O'Leary
ARN correspondent

Philosopher Cordelia Fine, who wrote a book on the neuroscience and other studies of the differences between men's and women's brains - and found most of them flawed - pauses to target a classic in evolutionary psychology: Why girls prefer pink.

... psychologists and journalists now speculate on the genetic and evolutionary origins of gendered color preferences that are little more than fifty years old.

Little more than how many years old? Read on:

For example, a few years ago an article in an Australian newspaper discussed the origins of the pink princess phenomenon. After trotting out the ubiquitous anecdote about the mother who tried and failed to steer her young daughter away from the pink universe, the journalist writes that the mother's failure "suggests her daughter was perhaps genetically wired that way" and asks, "is there a pink princess gene that suddenly blossoms when little girls turn two?"

Just in case we mistake for a joke the idea that evolution might have weeded out toddlers uninterested in tiaras and pink tulle, the journalist then turns to prominent child psychologist Dr. Michael Carr-Gregg for further insight into the biological basis of princess mania: "The reason why girls like pink is that their brains are structured completely differently to boys," he sagely informs us. "Part of the brain that processes emotion and part of the brain that processes language is one and the same in girls but is completely different in boys ... "

- Delusions of Gender: How Our Minds, Society, and Neurosexism Create Difference, p. 208.

Okay, but if Dr. Carr-Gregg and other authorities are correct, the pace of evolution has been nothing short of catastrophic in recent decades. Formerly, blue was the colour for girls - and for boys?:

The preferred color to dress young boys in was pink! Blue was reserved for girls as it was considered the paler, more dainty of the two colors, and pink was thought to be the stronger (akin to red). It was not until WWII that the colors were reversed and pink was used for girls and blue for boys... -Dress Maker Magazine

Certainly, in Kate Greenaway's late 19th century illustrations, fashionable girls strut in blue.

Fine also informs us that the early 20th century saw a concerted move to use infant and toddler clothes to reinforce gender differences. But that requires consumer choice. Most children's clothing of long ago was pretty functional - swaddling clothes, smocks, et cetera, and cut down adult clothes. Few people could afford dyes of their choice.

So yes, it's evolution - a very recent evolution of ideas about gender, which might depart with no offspring.

See also: Neuroscience: Philosopher rips "drivel" - pop science media 's bread and butter

More fun from voodoo neuroscience:

Neuroscience and popular culture: Who do voodoo? They do! Social neuroscientists, that is:

Neuroscience shows why women love shopping, why gay guys read maps like women, why jealous guys ... come to think of it, why does social neuroscience only tell us what we already heard from that high school drop-out cousin, shooting pool down in the rec room between his split shifts at the loading dock?

Is this really science? Probably not, say a team of statisticians, who took a look at some of these studies. Basically, many of the claimed correlations were simply too high to be possible. That was because the "social neuroscience" people were cherry picking the data."

Gender Genie: Fritz your wits about which sex you belong to?

Using an algorithm developed by Moshe Koppel, Bar-Ilan University in Israel, and Shlomo Argamon, Illinois Institute of Technology, you can find out whether the genie thinks you are a man or a woman by submitting a sample of your writing.

Given that the genie works best on texts of more than 500 words, I have decided to submit my five most recent columns for ChristianWeek.

Neuroscience: Vive la difference between boys and girls?

What I find really interesting is the way people are always looking for confirmation of weird theories from neuroscience, but they won't accept actual evidence that disconfirms a weird theory. For exmaple, there is way more evidence that boys and girls are different than that weird materialist theories of religion are true.

Incidentally, none of these findings shows that girls can't excel in math and science. They help us understand why many girls do not TRY to excel in math and science. That's useful information, however we choose to use it.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

by Denyse O'Leary
ARN correspondent

Once upon a time there was this bright philosopher and Fine writer who immersed herself in the pop culture sludge of the breathless (this just in!) latest findings of neuroscience on human nature, in this case the supposed differences between the way men and women think. Differences that, Fine argues, are poorly supported.

What I learned from Cordelia Fine's latest book: Add time on an fMRI scanner to a mediocre mind carrying out a conventional research program and you end up with fodder for Cowsmoopolitan. Fine found that the men vs. women studies were too badly done to be conclusive. Her survey removes all doubt as to how many magazine and newspaper editors, stuck for a Sunday featurette, ever even wonder about such matters.

She goes on to challenge neuroscientists on the ethics of passively allowing these shenanigans:

... neuroscientists who work in this area have some responsibility for how their findings of sex differences in the brain are interpreted and communicated. When this is done carelessly, it may have a real and significant impact on people's lives. Many neuroscientists do appear to be aware of this. They are appropriately cautious about interpreting sex differences to the brain, and may also take the time to remind journalists of just how far we are from mapping sex differences in the brain onto the mind. (And of course they may find their work being misrepresented, regardless, others, however, as we have seen, are more cavalier.) " - from Delusions of Gender: How Our Minds, Society, and Neurosexism Create Difference (p. 173)

On a less heartening note, she adds,

Finally, there's an urgent need for editors, journalists, and schools to develop far more skeptical attitudes toward claims about sex differences in the brain. It is appalling to me that one can, apparently, say whatever drivel one likes about the male and the female brain, and enjoy the pleasure of seeing it published in reputable newspaper,changing a school's educational policy, or becoming a best seller. - from Delusions of Gender: How Our Minds, Society, and Neurosexism Create Difference (p. 173)

Trouble is, Cordelia, drivel sells. The woman whose boyfriend is running around wants to believe that a brain scan shows that he is merely a less-evolved ape. And she may not have to wait long for "He's a Gorilla, You're a Bonobo, and You Two Make a Great Scream" (Whattafastbuck Press, 2011) to hit her local bookstore's Women's Empowerment Evening ...

It is really a moral question for the journalist, editor, and bookseller, whether - in hard times - to front this neurobullshipping or demand accountability.
Anyway, hats off to Fine for saying something.

Now, do I agree with Fine that there are no significant brain differences between men and women? Well, let's just say I have a different take on those differences, explained here.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

Dembski and Hitchens will debate the existence of a good God during a conference for the Biblical Worldview Institute at Prestonwood Christian Academy in Plano, Texas. Click here for the flyer...

by Denyse O'Leary
ARN correspondent

Recently, I advised readers of Jane Harris Szovan's new book on the shameful secrets of social Darwinist eugenics in Canada. The Alberta-based author tells me,

People have been asking me what Eugenics and the Firewall is about. Basically, it is about the history of eugenics in the Western countries. But it looks specifically at what happened in Alberta, how our province's somewhat bizarre political culture allowed it to happen (and why the vulnerable are still at risk for disaster, not just here but worldwide.) Then it compares Alberta to British Columbia, Saskatchewan and Ontario. Then, we look at how Alberta's experience compared to the rest of the Commonwealth, specifically the U.K. where forced sterilization was judged contrary to our shared constitution.(How a province in a dominion was allowed to get away with violating the constitution just shows how far the federal gov. will go in not challenging 'provincial rights.'

Hmmm, yes, it shows that for sure.* But it shows something else too.

Here is the gist of the book:

It's a dirty little secret the heirs to Alberta's populist legacy don't want Canadians to talk about.

In 1928 the non-partisan United Farmers of Alberta passed the first Sexual Sterilization Act. The UFA's successor, the Social Credit party, led by a radio-evangelist William Aberhart, and later by his protégé Ernest Manning, removed the need to obtain consent to sterilize "mental defectives" or Huntington's Chorea patients with dementia.

Between 1928 and 1972 nearly three thousand citizens were sterilized, lied to, experimented on, and subjected to daily abuse at the hands of provincial staff in Alberta. Most Albertans have forgotten the victims whose names made headlines in the 1990s, and politicians and pundits have shown little empathy for the victims.

The Eugenics Board horror story has largely been buried in Canada's mainstream national media. Conservative bloggers and columnists in Canada continue to blame the Liberals and CCF for Canada's barbaric eugenics program. The tar sands, oil royalties, health care budgets, environmental policies, and making sure the province's interests remain high on the federal agenda top the provincial headlines.

But the questions must be answered: How did a province that claims "strong and free" as its motto deny basic freedoms to so many of its own citizens? Why does the extent of Alberta's eugenics past and its link to the UFA/Social Credit legacy remain the unacknowledged moral blind spots in Canadian politics?

It's time to set the record straight.

It is past time. And from the fact that Harris Szovan's Google search stats spiked rapidly over the past 48 hours, I would guess that many know that.

Jane has quite reasonably been thinking/hoping that people won't go after her, but ... A straight record can mean crooked bunch. If you care about setting the record straight, spare a thought for her, and buy the book for a library and/or for yourself.

* They say this about us: If a Canadian species were in danger of extinction, the British would come up with matchless essays on the crisis, the French would fly Brigitte Bardot to scream up a storm on the ice pack, the Germans would write an encyclopedia about it, the Americans would set up a plan to save the species that cost three trillion dollars and employed one hundred thousand people ... And the Canadians? Oh, we'd spend ten years arguing about whether the species' woes are a federal or a provincial responsibility. That's part of how big problems get started here, when they do.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

by Denyse O'Leary
ARN correspondent

Jane Harris-Zsovan's book, Eugenics and the Firewall: Canada`s Nasty Little Secret n Shillingford, 2010) is now in print. It details the surprising reach of the compulsory sterilization movement in early twentieth century Canada. Many across the political spectrum participated, until the practice was finally derailed by informed public opinion and the courts.

The book's national launch will be Wednesday, November 17, 2010, 1:30-3:30, Galt Museum & Archives Store, Lethbridge, Alberta, Canada. Harris-Zsovan chose that locale because "the Galt archives have been helping me from time I wrote my first history paper at University."

Harris-Zsovan, who spent many hours poring over decades-old newspaper clippings, is bracing herself for controversy:

I'm inviting everyone I know and that includes people on the left, right and centre in Canada. I can't wait to see them all chit-chatting in the gallery at the Galt! I've warned them all that they will be uncomfortable with parts of this book. They seem okay with that so far. But I hope that discomfort leads to a healthy discussion.

Well, I hope so too. Many of us have found that discussion of eugenic sterilization - discussion that includes any mention of the social Darwinism that underlies it - often leads to the frantic defense of some Shrine to Evolution. To say nothing of attacks on anyone who offers evidence. Indeed, the spin now turns so fast that in the United States, museum goers are informed that Darwin was not a racist or eugenicist, when there is simply no escaping the facts of the case.

Anyway, Jane's is hardly a "take no prisoners" approach to unsavoury history:

I treat my home province, Alberta, B.C., and the architects of the only Sexual Sterilization Acts in the British Empire fairly gently. They made bad decisions, but we make worse ones. This behaviour continued from 1928 until 1972. (Actually it continued well after that until the Supreme Court put a stop to it.)

My sense is that too many people in Canada, generally a"low threat" society, assumed that it Couldn't Be Happening Here. Surprise, surprise.

Harris Zsovan is confident that

The lesson of the book: As bad as our past was, especially in Western Canada, we can be an example to other countries, most particularly the U.S. and Western Europe, if we own up to this.

Sure, Jane, if all Hull doesn't break loose first.

And if you think what happened in Canada was bad, consider what happened when social Darwinism hit Africa ...

Also just up at the Post-Darwinist:

Also just up at The Post-Darwinist:

When Social Darwinism found Africa ...

But then cats use a more subtle method for everything ...

Al Mohler vs. Mark Sprinkle: Is all this about being right or being nice?

Coffee!!: The evolutionary theory of why you feel smarter after a few beers

The very idea of design in the universe utterly obliterated: Chronicle 4382

New book: God and Evolution confronts the fan club of Darwin's unemployed God

At last: Chinese translation of By Design or by Chance? (But a question as well ...)

Top pundits: How can they score consistently higher than chance at being wrong?

Don't you feel better already, knowing that your innards are accidental globs of goo?

Very Weak Anthropic Principle: Is the Principle going, going, gone?

Christian Darwinism: Now you see the "Creator" and now you don't, but believe anyway

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

One only has to visit a tropical rainforest to discover a world filled with abundant treasures. It is entirely natural for people to want to protect these regions from any threat. Climate change has been perceived as a threat: cooler climates do not support tropical ecozones - but what about warmer climates? Concerns have been raised about plants being unable to adapt to the heat, and there are potential dangers of rainfall reductions. Geological research has revealed a remarkable period of Earth history at the Paleocene-Eocene Boundary, a very warm period known as the Paleocene-Eocene Thermal Maximum (PETM). Although this has been much studied, little is known of the way the tropics responded to high temperatures globally (temperatures rose by about 5 degrees C) and to higher levels of carbon dioxide (perhaps 2.5 times the present level). One point that is agreed is that this rise in global temperatures was geologically rapid: "one of the most abrupt global warming events of the past 65 million years". New research concludes that, fat from being compromised by heat stress, the tropical regions coped very well.

"Most scientists have assumed that, as carbon dioxide levels increase and the Earth warms, plant species diversity in the rainforests will start to dwindle, with plants unable to adapt to the heat. But a new study suggests that the opposite may be true. In the past, rising atmospheric carbon dioxide and higher temperatures actually drove the evolution of far greater numbers of new rainforest plant species than were wiped out."

Although the study says the Amazon can adapt to a warmer world, it still faces an extreme threat from deforestation. (Image: Gerd Ludwig/Corbis, Source here)

The fieldwork was located in Columbia and Venezuela and led by Carlos Jaramillo, a palaeobiologist at the Smithsonian Tropical Research Institute in Panama, In the late Paleocene, the northern Andes had not been uplifted and most of Central America was still underwater. Pollen recovered from cores was used to gain an understanding of the plants growing at the time.

"To find out how this ancient climate change affected rainforest plants, Jaramillo and his team analysed fossilized pollen trapped in rock cores from rainforests in Colombia and Venezuela. They spent seven years locating appropriate sites and taking samples, then used a battery of dating techniques to ensure that they were examining cores formed before, during and after the thermal maximum - a relatively narrow time window in geological terms. The results are published this week in Science."

The findings were an eye-opener. The researchers were expecting the abrupt warming event to have had adverse effects. However, Jaramillo is reported as saying: "we didn't find any extinction event [in plants] associated with the increase in temperature, we didn't find that the precipitation decreased". Furthermore, diversity increased.

"Although some plant species disappeared, many more new species arose. That included entire families, suggesting that the increased temperatures and carbon dioxide levels actually boosted biodiversity. "What we found was exactly the opposite of what we were expecting," says Jaramillo. "The diversity of the tropical forest increased really fast over a very short amount of time.""

With hindsight, the research outcomes are not so surprising. The authors point out in their paper that "Greenhouse experiments have shown that high levels of CO2 together with high levels of soil moisture improve the performance of plants under high temperatures, and it is possible that higher Paleogene CO2 levels contributed to their success." Fieldwork undertaken in forests has documented increased rates of growth that correlate with increased CO2 concentrations in the atmosphere (go here). The implication is that tropical forests are not as fragile and vulnerable to climate change as many have suggested.

"Indeed, it is possible that rainforest families in general, which have been present in the Neotropics since the Paleocene, have the genetic variability to cope with high temperatures, CO2, and rainfall."

Whilst these conclusions have primary applications in the fields of ecology and the environment, this blog is written to point out the relevance for a design-orientated perspective on the natural world. The clue is in the concept of "genetic variability" that enables animals and plants to adapt to environmental change. Within the Design paradigm, animals and plants are designed to adapt because the world's environments experience change. (Speciation, however, can often lead to a loss of genetic variability, which is why some species reach a state where environmental change threatens them with extinction.) This paradigm expects negative feedback mechanisms to be dominant in ecological systems (as pointed out here and here) so that perturbed systems are restored to an equilibrium state.

There is an important application to all this. Design thinking is relevant to many contemporary issues affecting human societies and the world's environments. I should add that there is no party line on such issues, and every view expressed is ultimately a personal view. Climate models have been developed that incorporate significant positive feedback mechanisms - allowing them to predict avalanche scenarios (whether heating or cooling). This has been accompanied by a strong emphasis on the fragility of the Earth's ecosystems - with consequent apocalyptic scenarios much loved by the media. These emphases have led to the politicisation of science, with climate scientists and many others advocating the expenditure of large sums of money to "save the planet". A design perspective allows us to look at the scientific evidence more dispassionately - and there are good reasons for rejecting climate models with large positive feedback parameters. It also allows us to have more confidence in the self-regulating character of the natural world. We recognise that climate change has always been an aspect of history, so adaptation to a changing world is the way forward.

Having said this, there is no doubt that human activity is affecting the Earth's ecozones in a damaging way. The biggest threat to tropical rainforests is not climate change but unmanaged logging. Governments are often complicit in this, and consumers are at fault whenever wood is purchased without any evidence that is from a managed forest source. Instead of blaming the consumption of fossil fuels, those concerned about tropical rainforests would do well to ensure the wood they purchase has the FSC trademark (or similar).

"Jaramillo believes that there is a more pressing threat to the diversity of tropical rainforests. "Deforestation is the real enemy," he says, "not the increase in temperature and carbon dioxide." "

Effects of Rapid Global Warming at the Paleocene-Eocene Boundary on Neotropical Vegetation
Carlos Jaramillo, Diana Ochoa, Lineth Contreras, Mark Pagani, Humberto Carvajal-Ortiz, Lisa M. Pratt, Srinath Krishnan, Agustin Cardona, Millerlandy Romero, Luis Quiroz, Guillermo Rodriguez, Milton J. Rueda, Felipe de la Parra, Sara Moron, Walton Green, German Bayona, Camilo Montes, Oscar Quintero, Rafael Ramirez, German Mora, Stefan Schouten, Hermann Bermudez, Rosa Navarrete, Francisco Parra, Mauricio Alvaran, Jose Osorno, James L. Crowley, Victor Valencia, and Jeff Vervoort.
Science, 330, 12 November 2010: 957-961

Abstract: Temperatures in tropical regions are estimated to have increased by 3 [deg] to 5[deg]C, compared with Late Paleocene values, during the Paleocene-Eocene Thermal Maximum (PETM, 56.3 million years ago) event. We investigated the tropical forest response to this rapid warming by evaluating the palynological record of three stratigraphic sections in eastern Colombia and western Venezuela. We observed a rapid and distinct increase in plant diversity and origination rates, with a set of new taxa, mostly angiosperms, added to the existing stock of low-diversity Paleocene flora. There is no evidence for enhanced aridity in the northern Neotropics. The tropical rainforest was able to persist under elevated temperatures and high levels of atmospheric carbon dioxide, in contrast to speculations that tropical ecosystems were severely compromised by heat stress.

See also:

Milton, J. Rapid warming boosted ancient rainforest, Nature News, 11 November 2010 | doi:10.1038/news.2010.604

A key concept for Darwinism is adaptation. Traits are identified that confer survival and reproduction advantages to an organism. These traits are supposed to experience selection pressures that drive adaptive change and speciation. Consequently, traits are of central importance for theories of evoplutionary transformation, as is also time. However, when contemplating the flowering plants, even Darwin found them difficult to reconcile with his theory. Writing to J.D. Hooker in 1879, he described the evolutionary success of angiosperms as "an abominable mystery". He was troubled by the abrupt origin and extraordinarily rapid diversification of flowering plants in the mid-Cretaceous.

"The answer to whether any of the above traits are consistent predictors of diversity of a given rate of lineage growth depends more upon geographical rather than biological traits, such as geographical extent (i.e., total area occupied by a clade) and climate. Others have suggested that neither geographical nor biological traits determine diversification on their own but rather certain traits (or combinations thereof) may stimulate diversification within a particular geographical context."

Darwin freely acknowledged weaknesses in his case for evolution by natural selection (Source here).

If branching speciation, as illustrated in Darwin's On the Origin of Species, and if there are no limits to the number of species possible (i.e. gradualism reigns), then a broad prediction can be made that the number of species within a clade will increase with clade age. A recent analysis of all families of flowering plants has looked for correlations like this but has failed to confirm this particular trend. Even allowing for statistical variations from the predicted pattern, the conclusion to be drawn is that clade age is no guide to species diversity.

"Drs. Jana Vamosi and Steven Vamosi of the Department of Biological Sciences have found through extensive statistical analysis that the size of the geographical area is the most important factor when it comes to biodiversity of a particular flowering plant family. The researchers were looking at the underlying forces at work spurring diversity - such as why there could be 22,000 varieties of some families of flowers, orchids for example, while there could be only forty species of others, like the buffaloberry family. In other words, what factors have produced today's biodiversity?"

The research considered all the 409 angiosperm families and amassed data on species richness. Four putative key traits were documented: growth form, fruit type, sexual system and floral symmetry. In addition, the researchers recorded the geographical range of the lineage and the area potentially available for expansion (based on an ecozone classification of biogeographical realms). Phylogenetic relationships were based on published angiosperm family trees and best estimates of their age of origin.

"In total, the procedures used here attempt to incorporate our broadest knowledge of angiosperm systematics to produce the most comprehensive phylogenetic hypothesis."

For people interested in the details of angiosperm diversity, there are some really interesting findings, including useful analyses of tropical ecozones. Our purpose here, though, is to focus on the main findings: species richness is primarily dependent on the geographical area colonised.

"Our analyses reveal that available area for expansion is the most critical determinant of increased diversification in flowering plants, followed by zygomorphy, as revealed by model-averaged estimates. Our best models consistently incorporated these features, explaining up to 51% of the variation in species richness. Age explained little of the variation in species richness, indicating diversity-dependent diversification consistent with previous studies. There was no indication that particular trait combinations, rather than isolated traits, lead to higher diversification rates."

The findings of this study are not out of step with other recent research. Vamosi and Vamosi refer to similar conclusions relating to passerine birds (published in 2006). Land vertebrates are discussed here, drawing the same conclusions. The Darwinian scenario of evolution by natural selection acting on inheritable variations is really a hypothesis that is failing to be validated by these analyses of data. Instead, we are witnessing a 'colonisation' theme emerging, in which animal and plant orders/families experience radiations influenced primarily by geography (and ecology).

"We find that several key traits are associated with species richness and geographical extent but that their effects are best seen when accounting for ecoregion area. These constraints on the 'carrying capacity' of a lineage are emerging as critically important in disparate lineages and placing the most severe bounds on the species richness of a lineage. Geography, thus, determines the species richness of a clade far more than age as lineages rapidly expand and diversify upon a landscape. Certain traits (herbaceousness and tropicality) encourage diversification by expanding the size of the landscape upon which diversification occurs. Once the landscape is 'full' of members of a particular family with a characterizing adaptation, speciation rates decline (or extinction rates increase) leaving both medium-aged and old-aged lineages with equivalent species richness."

For those of us who have questioned the efficacy of the Darwinian mechanisms so prominently promoted in textbooks, these new biodiversity studies are very interesting. They are opening the door for new perspectives on life's history - away from Darwinian adaptationism towards colonisation accompanied by relatively rapid diversification. The fossil record has never provided support for Darwinian transformation, but it does offer some fascinating scenarios of responses to global ecological change: abrupt appearance followed by rapid diversification and colonisation. Recent blogs exploring these issues have considered photosynthesizing plant communities in the late Precambrian, the first land plants (liverworts), land vertebrates, and planktic foraminifera. When these ideas get into the educational curriculum, the tendency to present everything from a Darwinian perspective will be challenged - alternatives are available and they demonstrate a better fit to available data.

Key innovations within a geographical context in flowering plants: towards resolving Darwin's abominable mystery
Jana C. Vamosi and Steven M. Vamosi
Ecology Letters, 13(10), 1270-1279, October 2010 | DOI: 10.1111/j.1461-0248.2010.01521.x

Abstract: Elucidating factors associated with diversification have been attempted in lineages as diverse as birds, mammals and angiosperms, yet has met with limited success. In flowering plants, the ambiguity of associations between traits and diversification has sparked debate since Darwin's description of angiosperm diversification as an 'abominable mystery'. Recent work has found that diversification is often diversity-dependent, suggesting that species richness depends on geographical area available more than on traits or the time available to accumulate species. Here, we undertake phylogenetic generalized least squares analyses that jointly examine the effects of age, ecoregion area and four ecological traits on diversification in 409 angiosperm families. Area explained the most variation, dwarfing the effect of traits and age, suggesting that diversity-dependent diversification is controlled by ecological limits. Within the context of area, however, traits associated with biotic pollination (zygomorphy) exhibited the greatest effect, possibly through the evolution of specialization.

See also:

Toward resolving Darwin's 'abominable mystery', EurekAlert (16 September 2010).

by Denyse O'Leary
ARN correspondent

In "Creationism lives on in US public schools" (New Scientist 20 October 2010), John Farrell revisits the Dover trial:

IN DOVER, Pennsylvania, five years ago, a group of parents were nearing the end of an epic legal battle: they were taking their school board to court to stop them teaching "intelligent design" to their children.

But the monster never sleeps, it seems:

None of this means that the Discovery Institute, the Seattle-based think tank that promotes intelligent design, has been idle. The institute helped the conservative Louisiana Family Forum (LFF), headed by Christian minister Gene Mills, to pass a state education act in 2008 that allows local boards to teach intelligent design alongside evolution under the guise of "academic freedom".

Who told these Cajuns that they have the same right to question Darwin as the Altenberg 16 or philosopher Jerry Fodor? Actually, no one should have the right, but definitely not Cajuns. And it gets worse all the time:

Five years after the landmark case, the battle for science education continues. But for the plaintiffs and their representatives this does not detract from the achievement. Their lead attorney, Eric Rothschild, sums it up: "If we'd lost, intelligent design would be all over the place now".

Earth to planet Rothschild: It already is.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

William Dembski, research professor in philosophy at Southwestern Baptist Theological Seminary, will spar with "anti-theist" Christopher Hitchens, known as a champion of the "new atheism," Nov. 18th.

Dembski and Hitchens will debate the existence of a good God during a conference for the Biblical Worldview Institute at Prestonwood Christian Academy in Plano, Texas. The debate will be hosted in the worship center at Prestonwood Baptist Church from 8:40 a.m. to 11:00 a.m. It will also be webcast on www.pcawebcast.com.

More...

Jay Richards writes in The American about Stephen Hawkings "nothing". Gravity seems to be a placeholder for a personal, eternal, intelligent designer. But, from whence came gravity? Using equivocal definitions of nothing gets you nowhere.

More...

Stephen Hawking has achieved the status of 'celebrity scientist'. He writes books that sell well and has both presented and performed in television series. His latest book, The Grand Design, co-authored with Leonard Mlodinow, has been reviewed widely by both popular press and scientific journals. According to Michael Turner, who wrote the Nature review, these authors:

"offer a brief but thrilling account of some of the boldest ideas in physics - including M-theory and the multiverse - and what these have to say about our existence and the nature of the Universe."

"How do we know that the reality we perceive is true?" - or are we like fish seeing the world from a bowl? (Graphic by Barron Storey, source here).

The media appeared to be stimulated primarily by the claim that physics has made God redundant. "God is unnecessary, science can explain the universe without the need for a creator" (BBC News), "Why God Did Not Create the Universe. There is a sound scientific explanation for the making of our world - no gods required." (Wall Street Journal). The Guardian responded by conducting a poll among its readers, asking the question: "Is physicist Stephen Hawking right that physics, not God, created the universe?" This theme is also picked out in the Nature review: "No miracle in the Multiverse". Some might find the argument to be artificially polarised - for did not the pioneers of science link the existence of laws of nature with the reality of a supreme Lawgiver? More recent research has unearthed evidence for the "fine-tuning" of the Cosmos, so the evidences of design have become more prominent with time. Hawking and Mlodinow recognise this when they write:

"Newton believed that our strangely habitable solar system did not "arise out of chaos by the mere laws of nature." Instead, he maintained that the order in the universe was "created by God at first and conserved by him to this Day in the same state and condition." The discovery recently of the extreme fine-tuning of so many laws of nature could lead some back to the idea that this grand design is the work of some grand Designer."

This brings us to the heart of the argument presented by Hawking and Mlodinow: they are endorsing M-theory and the Multiverse cosmological model. This is how Turner puts it:

"In searching for the holy grail, Hawking and others pinned their hopes first on super-gravity and then on string theory. Both are now seen as different regimes of a grander mathematical framework called M-theory, where M is yet to be determined - is it master, miracle or mirage? M-theory unifies gravity with the other fundamental forces (weak and strong nuclear and electromagnetism), predicts seven additional dimensions of space and suggests that space and time might be emergent phenomena rather than fundamental. It is exciting and important, but much of it remains to be explored."

Using M-theory, cosmologists have suggested that our universe is but one of a vast number of universes, all with different physics and with different life-histories. We happen to be in one that has the parameters that favour life. The fine tuning is not by design, but by chance. When you have an infinity of options, anything is theoretically possible! Hawking and Mlodinow explain it this way:

"As recent advances in cosmology suggest, the laws of gravity and quantum theory allow universes to appear spontaneously from nothing. Spontaneous creation is the reason there is something rather than nothing, why the universe exists, why we exist. It is not necessary to invoke God to light the blue touch paper and set the universe going. Our universe seems to be one of many, each with different laws. That multiverse idea is not a notion invented to account for the miracle of fine tuning. It is a consequence predicted by many theories in modern cosmology. If it is true it reduces the strong anthropic principle to the weak one, putting the fine tunings of physical law on the same footing as the environmental factors, for it means that our cosmic habitat - now the entire observable universe - is just one of many. Each universe has many possible histories and many possible states. Only a very few would allow creatures like us to exist. Although we are puny and insignificant on the scale of the cosmos, this makes us in a sense the lords of creation."

Some of us will continue to think that the multiverse advocates are driven by a theological agenda: the need to account for the miracle of fine tuning. The theories of modern cosmology are being selected by intelligent agents: they have other options. But atheism is driving these agents to find responses to the strong evidences of design which are staring them in the face. This blog is arguing that they are on a road that leads to the destruction of all that we value within science. The first casualty is testability and the falsification criterion. This is where Turner finds a problem (and for more on this point, John Horgan's blog is worth reading):

"The multiverse is possibly the most important idea of our time, and may even be right, but it gives me a headache. Is it science if we cannot test it? The different patches are incommunicado, so we will never be able to observe them. The multiverse displaces rather than answers the question about choice and who chooses, and does not explain why there is something rather than nothing."

Secondly, the concept of realism in science is sacrificed. This is the focus of the article Hawking and Mlodinow wrote for Scientific American. In the quest for a theory of everything (that explains our Cosmos), they have adopted a theory with a seemingly infinite number of solutions. M-theory never leads to a unique set of equations. Every implementation of the theory is accompanied by its own dependent reality. Consequently, it does not make sense to talk of what "reality" actually is.

"In our view, there is no picture- or theory-independent concept of reality. Instead we adopt a view that we call model-dependent realism: the idea that a physical theory or world picture is a model (generally of a mathematical nature) and a set of rules that connect the elements of the model to observations. According to model-dependent realism, it is pointless to ask whether a model is real, only whether it agrees with observation. If two models agree with observation, neither one can be considered more real than the other. A person can use whichever model is more convenient in the situation under consideration."

Thirdly, we are presented with a cosmological extrapolation of quantum mechanics. The authors are so captivated by their theoretical models that they have lost touch with the need to constrain their thinking by reference to empirical data. This is from a review in The Economist:

"The main novelty in "The Grand Design" is the authors' application of a way of interpreting quantum mechanics, derived from the ideas of the late Richard Feynman, to the universe as a whole. According to this way of thinking, "the universe does not have just a single existence or history, but rather every possible version of the universe exists simultaneously." The authors also assert that the world's past did not unfold of its own accord, but that "we create history by our observation, rather than history creating us." They say that these surprising ideas have passed every experimental test to which they have been put, but that is misleading in a way that is unfortunately typical of the authors. It is the bare bones of quantum mechanics that have proved to be consistent with what is presently known of the subatomic world. The authors' interpretations and extrapolations of it have not been subjected to any decisive tests, and it is not clear that they ever could be."

Paradoxically, scientific realism has been used to promote atheism against theism, but Hawking is now leading his band of atheists towards a virtual reality dream-world that is generated by the manipulation of mathematical models. With science developing independently of the empirical world, realism becoming localised and history becoming a construct of observation, post-modernist thinking reigns supreme. Now it is time for theistic realists to quote Sagan's words with conviction:

"For me, it is far better to grasp the Universe as it really is than to persist in delusion, however satisfying and reassuring." (Carl Sagan, The Demon-Haunted World (1995) Chapter 1)

No miracle in the Multiverse
Michael Turner
Nature, 467, 657-658 (7 October 2010) | doi:10.1038/467657a

1st paragraph: Despite publicity to the contrary, The Grand Design does not disprove the existence of God. Science has not had much new to say about God since mathematician Pierre-Simon Laplace remarked to Napoleon that he had no need for "that hypothesis" when asked why he had neglected the deity in his treatise Mecanique celeste (Celestial Mechanics, 1799-1825).

The Elusive Theory of Everything
Stephen Hawking and Leonard Mlodinow
Scientific American, October 2010.

1st paragraph: A few years ago the city council of Monza, Italy, barred pet owners from keeping goldfish in curved fishbowls. The sponsors of the measure explained that it is cruel to keep a fish in a bowl because the curved sides give the fish a distorted view of reality. Aside from the measure's significance to the poor goldfish, the story raises an interesting philosophical question: How do we know that the reality we perceive is true?

See also:

Lennox, J., As a scientist I'm certain Stephen Hawking is wrong. You can't explain the universe without God. The Daily Mail, 3rd September 2010.

Tyler, D. The Metaphysics of Multiverse Theory, ARN Literature Blog (20 November 2008).

by Denyse O'Leary
ARN correspondent

This post was about an atheist facing death, and it is inspiring. This one is about an atheist blowhard - an evolutionary biologist who seems determined, so far as I can see, to collapse in the ruins of Darwinism. Some excerpts from Jerry A. Coyne's "Religion in America is on the defensive" (USA Today, October 11, 2010):

Atheist books such as The God Delusion and The End of Faith have, by exposing the dangers of faith and the lack of evidence for the God of Abraham, become best-sellers. Science nibbles at religion from the other end, relentlessly consuming divine explanations and replacing them with material ones. Evolution took a huge bite a while back, and recent work on the brain has shown no evidence for souls, spirits, or any part of our personality or behavior distinct from the lump of jelly in our head. We now know that the universe did not require a creator. Science is even studying the origin of morality. So religious claims retreat into the ever-shrinking gaps not yet filled by science. And, although to be an atheist in America is still to be an outcast, America's fastest-growing brand of belief is non-belief.

As neuroscientist Mario Beauregard and I demonstrate in The Spiritual Brain, materialist explanations have utterly failed in explaining the human mind. They continue to ail even as I write and you read, with one limp speculation after another.

Soft! There is ancient evil about:

But faith will not go gentle. For each book by a "New Atheist," there are many others attacking the "movement" and demonizing atheists as arrogant, theologically ignorant, and strident.

Well, if so, you just heard from Exhibit 1.

It gets better:

Science operates by using evidence and reason. Doubt is prized, authority rejected. No finding is deemed "true" - a notion that's always provisional - unless it's repeated and verified by others. We scientists are always asking ourselves, "How can I find out whether I'm wrong?"

To that, I can only reply Climategate, which made clear that a number of key climate scientists were willing to manipulate the system to insert their opinion contra evidence. And in the age of Signature in the Cell (Harper One, 2009), Expelled (about attempts to suppress findings that contradict atheist materialism) did not help the new atheists' image.

My favourite lines are

And this leads to the biggest problem with religious "truth": There's no way of knowing whether it's true. I've never met a Christian, for instance, who has been able to tell me what observations about the universe would make him abandon his beliefs in God and Jesus. (I would have thought that the Holocaust could do it, but apparently not.) There is no horror, no amount of evil in the world, that a true believer can't rationalize as consistent with a loving God. It's the ultimate way of fooling yourself. But how can you be sure you're right if you can't tell whether you're wrong?

Well, if one does not believe that one's mind has an independent reality, one cannot tell whether anything at all is right or wrong. After all, if morality is all about survival of the fittest, then there is no morality, only survival of the fittest.

The funniest part is this:

Out of 34 countries surveyed in a study published in Science magazine, the U.S., among the most religious, is at the bottom in accepting Darwinism: We're No. 33, with only Turkey below us.

Well, the United States put men on the moon, mapped the outer planets, and generally leads in science. And it is more religious than other countries. So, if religion makes a difference, bring it on.

The real lesson is that leading nations lead. They can lead in both science and religion. There are nations out there having a fit about both.

More on the new atheism (atheism on stilts):

The new atheists: Santa's sleigh came and went, and never gave them what they needed

Salvo 7: Just released edition features batty bioethicists, suckered scientists, senseless psychologists ...
(And we don't mind sayin' it either.)

Imagine no Religulous

Also just up at The Mindful Hack, my blog on neuroscience and spirituality issues:

African religion: Begin by trying to understand

Media and religion: If people cannot safely say what they think, what effect can media have?

Christopher Hitchens: Attempting the good death without God

Branded but stranded? How seriously does Generation Y really take brands?

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

By Robert Deyes
ARN Correspondent

The blogosphere is brimming with commentaries over the ever-visible changes that usher in the arrival of Autumn in the northern hemisphere (1). The beckoningly bright colors of the foliage on our trees and the seasonal appearance of pumpkins that adorn our porches and abound in the fields around our cities serve as reminders of a festive transition. Throw the occasional honking of migrating Canadian geese into the mix and it is easy to see why many of us cannot help but momentarily stop in awe. The geese in particular are my gaze-catchers. Craning my neck as I look straight up I have become obsessed with capturing the flight of these birds on camera.

But there is more that interests me about Canadian geese than simply their migratory 'order of business'. Unknown to many a bird watcher, Canadian geese are one of several 'gold mine' species that harbor a strain of bacteria called Bacillus licheniformis in the tufts of their plumage (2). These feather-degrading bugs are prevalent in all manner of ground-foraging birds and occur in greatest numbers during the late autumn and winter months. Because of their tough keratin-rich microfibril composition, feathers are extraordinarily resistant to biodegradation (2). But not so tough that keratinolytic bacteria such as B. licheniformis cannot break them down (2). And biotechnologists are exploiting this ability to the full.

B. licheniformis has spawned much excitement in the agricultural world (3). Bird feathers are routinely used in animal feed. But until the early 1990s steaming was the only means by which they could be made more digestible (3). Scientific acumen and ingenuity changed all that. By putting B.licheniformis to work on a feathery meal, an inter-disciplinary group from North Carolina State University generated "appreciable degradation products" of digestible protein (3). In so doing they opened the door for a commercially-viable process that improves on the nutritional value of traditional steaming methods.

And its agricultural relevance has not stopped there. This multi-purpose bacterium is also finding application in pest control as a pre-harvest treatment for eradicating diseases that attack fruit (4). Mangos, which today constitute "one of the most important fruit crops grown in tropical and subtropical regions" have been targeted for trials against bacterial blackspot (Xanthomonas campestris), anthracnose and soft rot (4). Chemical treatments such as Copper Oxychloride have been heavily legislated against because of their detrimental effects on soils (4). B.licheniformis has proven to be an effective antagonist against these diseases and is therefore gaining traction as the way of the future for pest control.

Enzymes are commonly deployed in laundry products where they function as potent digesters of dried-on grime. And those of B.licheniformis are best-in-class when it comes to getting the job done. Look down the ingredients list of most brands of washing powder and you are likely to find two components- alpha-amylase and Subtilisin-A- that respectively perform the job of breaking down starch and proteins (5). Thankfully detergents do not adversely affect the ability of these enzymes to get to work on food splurges (6). Microbially-derived proteases form more than half of the industrial enzyme market (6). And those of alkaline-dwelling organisms such as B.licheniformis are particularly attractive given the high pH of laundry detergents (9.0-12.0) (6).

B.licheniformis has also joined a fast growing club of microorganisms able to synthesize gold nanoparticles which are used in the development of pharmaceuticals (7). Microorganisms such as B.licheniformis carry periplasmic proteins on their outer surface that bind and reduce Aureum Chloride and in the process generate 10-100nm sized nanoparticles that can be isolated from the bacterial fraction as a dried powder (7). The microorganismic approach to gold nanoparticle production has the unique advantage of being more ecologically sound than current procedures that use harmful reducing agents (7).

From our houses to our farms and onwards into the pharmaceutical development lab B.licheniformis is fast becoming an indispensable workhorse. Its many secrets are being exploited in novel ways. And its revolutionary attributes continue to amaze. Higher eukaryotes sport elaborate olfaction mechanisms to detect gas molecules (8). Up until earlier this year there had been no reports of similar mechanisms in bacteria (8). All that changed with the news that a couple of European biotechnologists had incontrovertibly demonstrated olfaction in B.licheniformis cultures (8). By putting B.licheniformis adjacent to inducer strains of B.subtilis, M.luteus and E.coli, Reindert Nijland and J. Grant Burgess observed notable color changes and a tendency for formation of dense pellicles (known in the trade as biofilms) (8,9). Some simple experiments gave Niijland and Burgess the clues they needed to home in on the molecular exchange that lay at the heart of this response- a rise in concentrations of gaseous ammonia (8,9).

Seen in the wider context of the discoverability of our planet that authors such as Guillermo Gonzalez, Jay Richards and Michael Denton have exposed in their best-selling tomes, B.licheniformis is just one of a vast number of available resources that are helping us reshape the way we live. "The stupendous success of science since 1600" writes Denton "is testimony enough to the remarkable fitness of our mind to comprehend the world" (10). "We've seen that scientific progress and discovery depend on nature being more than meaningless matter in motion...It's an exquisite structure that preserves vast stores of information...We in turn possess the materials and the physical and intellectual capacity to create technologies...As eyeglasses and light bulbs have improved our ability to read written texts so the microscope and telescope have allowed us to read the book of nature more deeply...The myriad conditions that make a region habitable are also the ones that make the best overall places for discovering the universe in its smallest and largest expressions" (11).

Whether the olfaction aptitude of B.licheniformis can be translated into a useful application that aids in the "betterment of human life" (in accordance with the biotechnologists' mantra, 12) remains to be seen. Yet the story of this robust microorganism seems far from over. And as the geese continue to pass overhead during this year’s autumnal leaf-fall I cannot help but see it as a bacterial 'high-flyer' that has taken center stage in the biotechnology arena.

Further Reading

1. Sara Klink (2010) A Time For Harvest, Promega Connections, September, 24th, 2010, See http://promega.wordpress.com/2010/09/24/a-time-for-harvest/

2. Edward Burtt, Jann Ichida (1999) Occurrence of feather-degrading bacilli in the plumage of birds, The Auk, See http://findarticles.com/p/articles/mi_qa3793/is_199904/ai_n8834646/

3. C.M.Williams , C.S Richter, J.M. MacKenzie Jr, Jason C.H. Shih (1990) Isolation, Identification and Characterization of a Feather-Degrading Bacterium, Applied And Environmental Microbiology, Volume 56 (6), pp. 1509-1515

4. Evaluation of pre-harvest Bacillus licheniformis sprays to control mango fruit diseases, Crop Protection, Volume 26, pp. 1474-1481

5. Measurement of endo-Protease and Þ±-Amylase in Biological Washing Powders & Liquids using AZO CASEIN and AMYLAZYME TABLETS www.megazyme.com/GetAttachment.aspx?id=17e0f84c-9ba1

6. Nedra El Hadj-Ali, Rym Agrebi, Basma Ghorbel-Frikha, Alya Sellami-Kamoun, Safia Kanoun and Moncef Nasri (2007) Biochemical and molecular characterization of a detergent stable alkaline serine-protease from a newly isolated Bacillus licheniformis NH1, Enzyme and Microbial Technology, Volume 40, pp. 515-523

7. Kalimuthu Kalishwaralal, Venkataraman Deepak, Sureshbabu Ram Kumar Pandian, Sangiliyandi Gurunathan (2009) Biological Synthesis Of Gold Nanocubes From Bacillus Licheniformis, Bioresource Technology, Volume 100, pp. 5356-5358

8. Reindert Nijland and J. Grant Burgess (2010) Bacterial Olfaction, Biotechnology Journal, DOI 10.1002/biot.201000174

9. Janelle Weaver (2010) Bacteria sniff out their food, Nature 16 August 2010, See http://www.nature.com/news/2010/100816/full/news.2010.411.html

10. Michael Denton (1998) Nature's Destiny: How The Laws of Biology, Reveal Purpose in the Universe, 1st Edition Published by the Free Press, New York, p.260

11. Guillermo Gonzalez and Jay Richards (2004) The Privileged Planet, How Our Place In The Cosmos Is Designed For Discovery, Regnery Publishing Inc, Washington D.C, New York, p.334

12. Abdelali Haoudi (2003) New Forum for Innovative Research in Biomedicine and Biotechnology, J Biomed Biotechnol. 2003, Issue 3, p.161

Justin Brierley, host of Premier Christian Radio's popular faith debate programme Unbelievable? will host "An Evening with Michael Behe" on Monday, 22 November at Westminster Chapel in central London.

For all the information you will need to attend this event...

http://www.premier.org.uk/behe

For more information on the entire Darwin or Design? tour...

http://www.darwinordesign.org.uk/

According to Massimo Pigliucci and Maarten Boudry, the widespread use of machine-information metaphors is unfortunate and misleading. They complain about textbooks that develop metaphors to a considerable level of detail. As an example, they cite Alberts, who is often quoted for his analogy between a cell and a "miniature factory, complete with assembly lines, messengers, transport vehicles, etc." Another machine metaphor they dislike is that of the genome as a "blueprint", notably in the hype surrounding the Human Genome Project. Whilst these analogies are widely held within the scientific community and by educators, the main target of Pigliucci and Boudry's paper appears to be intelligent design:

"The analogy between living organisms and man-made machines has proven a persuasive rhetorical tool of the ID movement. In fact, for all the technical lingo and mathematical 'demonstrations', in much of their public presentations it is clear that ID theorists actually expect the analogies to do the argumentative work for them. In Darwin's Black Box, Behe takes Alberts' machine analogy to its extreme, describing the living cell as a complicated factory containing cargo-delivery systems, scanner machines, transportation systems and a library full of blueprints."

From the Editorial of Molecular Cell (October 2010): "Looking at a textbook picture of a cell, it all seems perfectly serene within, like a bird's eye view of a beautiful city. Zooming in close, however, a much more dynamic image emerges (see the cover). It soon becomes apparent that cells encounter a wide variety of conditions, many of which can induce stresses. These insults must be carefully and appropriately dealt with to maintain the balance that is needed for cell survival and growth." (Source here)

Pigliucci and Boudry rightly trace the emergence of machine metaphors back to, at least, the Middle Ages, and a rise to prominence with the rise of science in the 17th Century. The well-known analogy made by William Harvey is mentioned: the human heart is a pump. The authors also rightly point out that the scientists of the time gave these metaphors some additional substance, because they considered human designs to be imaging designs of the Creator.

"For Newton and many of his contemporaries, the importance of the mechanical conception of nature was greater than the mere term 'metaphor' would suggest, as the development of mechanistic philosophy was itself largely inspired by religious motivations. As Shanks wrote in his account of the history of the design argument, "the very employment of machine metaphors invited theological speculation"."

The authors turn to David Hume to find arguments foreshadowing the demise of design inferences made by the science community. Hume's (1779) Dialogues concerning natural religion is said to expose "several problems with the central analogy". The key thought is that our experience of design is limited to human artifacts, and it is presumptuous to extrapolate from this and make statements about design in general and God's design in particular.

"Hume realized that, at least in some cases, appearances of intelligent design can be deceptive. [. . .] Although Hume does not deny that we can discern similarities between nature and human artifacts, he warns us that the analogy is also defective in several respects. And if the effects are not sufficiently similar, conclusions about similar causes are premature. [. . .] Aware of the fallibility and imperfections of human reasoning, Hume remains highly skeptical about the design inference and the machine analogy, even though he was not able to provide a satisfactory explanation for the appearance of design in nature."

It has always surprised me that David Hume's arguments are considered weighty. The preceding generations of scholars did have a rationale for thinking that there is a relationship between the Creator's design and human design. This was based on the concept of image-bearing, drawn from the Judeo-Christian worldview of the time. If man is made in the image of God, they reasoned, then we design because God designs, and analogies can be drawn between human design and design in nature. Science became, for Johannes Kepler as for them all, "thinking God's thoughts after him".

The real challenge came when the theistic worldview of the pioneers of science was replaced by the deistic worldview of the Enlightenment scholars and the naturalistic worldview of their heirs. Only then does Hume's argument become coherent - and even then, design inferences can still be made at the level of hypotheses that can be tested and potentially falsified.

However, Pigliucci and Boudry suggest these metaphors and analogies are bad science. This needs to be examined closely. They object to the 'cell as a factory' analogy, the 'genome as blueprint' analogy, the 'bacterial flagellum as rotary motor' analogy, and the 'biochemical processes as digital characters in a machine code' analogy. Significantly, all these examples relate primarily to our understanding of how cells function. The major objections to metaphors, however, are linked to theories of development and the need for a viable theory of evolutionary transformation. This gives the clue to the real argument of this paper: Pigliucci and Boudry want to show that the neodarwinian synthesis and genetic reductionism have failed to deliver answers to the real problems of development and evolution, and the popular 'genome as blueprint' metaphor is inhibiting the critical appraisal of existing theory.

The 'blueprint' metaphor receives extensive discussion. They say that wherever it is used, it is always in the context of molecular biology research, not the organism as a whole. They claim that many biologists are concerned about the "hyper-reductionist approach brought about by the molecular revolution". With new discoveries about gene regulation and epigenetics, the blueprint metaphor is looking increasingly limited in its application.

"[N]ew ways of thinking about development and evolution are building a conceptual vocabulary that increasingly distances itself from the machine-information metaphor. [. . .] An answer that is being explored successfully is the idea that the information that makes development possible is localized and sensitive (as well as reactive) to the conditions of the immediate surroundings. In other words, there is no blueprint for the organism, but rather each cell deploys genetic information and adjusts its status to signals coming from the surrounding cellular environment, as well as from the environment external to the organism itself."

The need to move beyond classical genetics is even more pressing when we turn our attention from development to evolution. At best, neodarwinism is perceived to provide relatively few of the answers needed. The "current frontiers of theoretical evolutionary biology" have moved. Further comments on this are found here and here.

An example from Pigliucci and Boudry follows.

"Eva Jablonka and Marion Lamb have gone in some sense a step further and attempted to formalize a broader view of evolutionary change, which depends on the existence of not one but four mechanisms of inheritance: first, the standard genetic system; second, a panoply of epigenetic heritable effects, based on recently or newly discovered phenomena, such as differential methylation of genes, alterations of chromatin structure, so-called interference RNAs,7 and changes in conformation of proteins (e.g., prions), to mention a few; third, behavioral inheritance, mediated through the ability of some animal species to mimic each other's behavior without having it to be "inscribed" in their genes; and fourth cultural inheritance, which is limited to humans and perhaps a few other species of primates, but which has had an obviously disproportionate effect on the recent history of our planet."

The conclusion of all this is that education and research needs to refocus: away from the molecular revolution which is proving increasingly unproductive.

"The preceding discussion, we argue, shows that the limitations intrinsic in metaphors such as 'genes as blueprints' and the like are not just deleterious for science education - which would be bad enough. They actually misdirect or partially derail thinking about what sort of research programs biologists ought to carry out and how. While there is no question that the "molecular revolution" has been a central and positive development in biology, and indeed in science in general, throughout the second part of the 20th century, it is also becoming increasingly clear that the ultra-reductionist approach inspired and fueled by machine-information metaphors is running out of steam and needs to be replaced with more sophisticated and realistic thinking (a kind of reasonable, or non-greedy reductionism, so to speak). Is it then time to retire metaphors like blueprints and machines, and to seek an alternative way to conceptualize biological organisms, or would it perhaps be better to abandon the use of metaphors in this field altogether?"

Anyone reading the abstract of this paper would think that the "bad science" references relate to ID arguments. However, this is not the focus of their arguments! The authors are actually writing about the failure of the Modern Synthesis to understand both development and the processes of evolutionary transformation. They spend most of their critical discussion on the 'genome as blueprint' metaphor. It may surprise most readers to know that few, if any, ID scholars use the analogy outside the context of protein synthesis within the cell. They do not use this metaphor to suggest that the blueprint comprehends all aspects of reproduction and development. I am familiar with ID scholars questioning genetic-reductionism along the lines followed by Pigliucci and Boudry, and arguing that development needs some information-rich organismally-orientated thinking. Similarly, ID scientists critique the approach of the Modern Synthesis to evolutionary theory in much the same way as Pigliucci and Boudry have done. So there is much common ground here. The main complaint appears to be that ID scientists use metaphors to suggest that natural objects are actually intelligently designed. They are comfortable with the thought that the living world evidences features that bear witness to intelligent agency. They make use of analogies between human designs and natural phenomena because they infer intelligent agency for both categories. However, this has not led to bad science. Allowing that analogies are always partial, there should be no difficulty recognising the immense benefits that have come to science by pursuing this approach. Historical examples are easy to find; some recent examples are here and here and here.

Why Machine-Information Metaphors are Bad for Science and Science Education
Massimo Pigliucci and Maarten Boudry
Science and Education, Online October 2010 | DOI: 10.1007/s11191-010-9267-6

Abstract: Genes are often described by biologists using metaphors derived from computational science: they are thought of as carriers of information, as being the equivalent of "blueprints" for the construction of organisms. Likewise, cells are often characterized as "factories" and organisms themselves become analogous to machines. Accordingly, when the human genome project was initially announced, the promise was that we would soon know how a human being is made, just as we know how to make airplanes and buildings. Importantly, modern proponents of Intelligent Design, the latest version of creationism, have exploited biologists' use of the language of information and blueprints to make their spurious case, based on pseudoscientific concepts such as "irreducible complexity" and on flawed analogies between living cells and mechanical factories. However, the living organism = machine analogy was criticized already by David Hume in his Dialogues Concerning Natural Religion. In line with Hume's criticism, over the past several years a more nuanced and accurate understanding of what genes are and how they operate has emerged, ironically in part from the work of computational scientists who take biology, and in particular developmental biology, more seriously than some biologists seem to do. In this article we connect Hume's original criticism of the living organism = machine analogy with the modern ID movement, and illustrate how the use of misleading and outdated metaphors in science can play into the hands of pseudoscientists. Thus, we argue that dropping the blueprint and similar metaphors will improve both the science of biology and its understanding by the general public.

The Guardian reports that Gideon Sa'ar, the education minister who installed Avital as his chief scientist on a "trial period" last December, dismissed the former head of aeromechanics at defence firm Elbit Systems and member of the right-leaning Professors for a Strong Israel, over his statements "denying the tenets of evolution and global warming". (Avital also unsuccessfully ran for Sa'ar's Likud party in the 2006 Knesset elections.)

The paper reports a ministry official as saying: "Someone who holds the opinions of Avital cannot serve as chief scientist of the education ministry."

More...

by Denyse O'Leary
ARN correspondent

A number of red flags have shot up recently about comfy relationships between science, media, and corporate interests. Here's a small batch to contemplate:

- Elizabeth Landau asks at CNN, "Where's the line between research and marketing?" (October 13, 2010):

JAMA, one of the premier peer-reviewed health publications in the United States, published the Jenny Craig-funded study that had to do with -- surprise! -- women losing weight in the Jenny Craig weight-loss program. The study found that women in the Jenny Craig program lost between three and four times as much weight as those who dieted independently.

Fontanarosa says the study passed the journal's requirements for a privately funded study: the sponsor - Jenny Craig - tried to minimize its influence over the management analysis of data and reporting of the findings. An academic investigator had access to all data, and an academic biostatistician conducted the analysis.

But some experts say the public should have extra skepticism than when viewing the results of a study like this.

The experts' further advice, as properly recounted by Landau, is no substitute for plain old hardline skepticism. Here's some skeptical advice on weight loss programs in general.

- In "Lies, damn lies, and medical science"(The Atlantic, November 2010) David H. Freedman reports on the shifting sands of health dangers uncovered by peer-reviewed studies:

That question has been central to Ioannidis’s career. He’s what’s known as a meta-researcher, and he’s become one of the world’s foremost experts on the credibility of medical research. He and his team have shown, again and again, and in many different ways, that much of what biomedical researchers conclude in published studies—conclusions that doctors keep in mind when they prescribe antibiotics or blood-pressure medication, or when they advise us to consume more fiber or less meat, or when they recommend surgery for heart disease or back pain—is misleading, exaggerated, and often flat-out wrong. He charges that as much as 90 percent of the published medical information that doctors rely on is flawed. His work has been widely accepted by the medical community; it has been published in the field’s top journals, where it is heavily cited; and he is a big draw at conferences. Given this exposure, and the fact that his work broadly targets everyone else’s work in medicine, as well as everything that physicians do and all the health advice we get, Ioannidis may be one of the most influential scientists alive. Yet for all his influence, he worries that the field of medical research is so pervasively flawed, and so riddled with conflicts of interest, that it might be chronically resistant to change—or even to publicly admitting that there’s a problem.

[ ... ]

It didn’t turn out that way. In poring over medical journals, he was struck by how many findings of all types were refuted by later findings. Of course, medical-science “never minds” are hardly secret. And they sometimes make headlines, as when in recent years large studies or growing consensuses of researchers concluded that mammograms, colonoscopies, and PSA tests are far less useful cancer-detection tools than we had been told; or when widely prescribed antidepressants such as Prozac, Zoloft, and Paxil were revealed to be no more effective than a placebo for most cases of depression; or when we learned that staying out of the sun entirely can actually increase cancer risks; or when we were told that the advice to drink lots of water during intense exercise was potentially fatal; or when, last April, we were informed that taking fish oil, exercising, and doing puzzles doesn’t really help fend off Alzheimer’s disease, as long claimed. Peer-reviewed studies have come to opposite conclusions on whether using cell phones can cause brain cancer, whether sleeping more than eight hours a night is healthful or dangerous, whether taking aspirin every day is more likely to save your life or cut it short, and whether routine angioplasty works better than pills to unclog heart arteries.

Go here for more.

- And don't expect the legacy mainstream media to run to help. Too many of them are part of the pattern themselves, as Paul Raeburn at Knight Journalism Tracker points out:

Yesterday, I criticized the foundation for taking funding from Pfizer for its “all-expenses-paid” annual cancer conference for reporters.

This morning, I looked at the press foundation’s donors. In its 2009 annual report, the foundation said “nearly 300 journalists benefitted from our training in Washington, around the world, online and through webinars. And it boasted that “in one of the tumultuous years in the U.S. media business, we did all this without charging journalists a dime, with programs that received some of our highest evaluations ever.”

How did the National Press Foundation do it?

Raeburn figures they did it because pharmaceutical corporations contributed about one quarter of the money and the journalism organizations' contributions were "far smaller." He adds,

When the National Press Foundation says in its annual report that it is funded, in part, by “concerned corporations,” it’s right on the money. You can bet that Pfizer, Merck, and the others are concerned about what appears in the press!

No kidding. The corruption here isn't open, it's insidious. The questions one does not ask, the research one does not do, the people one knows better than to confront, the backing down and the sliding away ... Sound familiar, anyone?

Do I say peer review is bad? No, but it can be useless or misleading. The key problem is that it is treated as a seal of approval. Yet it can often be the means by which third rate stuff gets attention and serious stuff is suppressed. The system is now corrupt enough that one can no longer take seriously claims like "Orthodox science doesn't accept this." My immediate response is, "Is THAT all you got by way of objection?"

I have written about the peer review scandal elsewhere:

"Peer review, mere review, and smear review"

"Peer review: Life, death, and the British Medical Journal"

Science: A year-end wad of fraud, falsified data, and other award-winning tenure strategies ...

Peer review: What if your peers would have to be otherconspiracy theorists? (No, really!)

Peer review: Gold standard or gold in "them thar hills"

* In fairness, journalism has been hit hard in recent years by layoffs, etc. But that's when we should just hold cheaper conferences and lump it until good stories start making money again.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

The earliest macrofossils of plants occur in the Silurian Period of Earth history. However, palynology (the study of plant spores, pollen and particulate organic matter in rocks) has pushed the history of plants back to the Middle Ordovician. Newly reported work has documented spores in strata that are dated 8-12 Ma earlier that the previous record holder. Both the research paper (Rubinstein et al. 2010) and the commentary (Wellman 2010) present the findings within a framework of evolutionary transformation. Press coverage puts it this way:

"As land plants matured, they evolved from liverworts into mosses, and then into plants known as hornworts and lycopods. Then ferns appeared before seed plants, of which there are many species today, finally evolved."

Liverworts are ideally suited for colonising barren ground (source here)

The concept of evolution as a 'maturing' trend is itself loaded with cultural baggage. People read into the concept all sorts of ideas that are not explicit or implied by the theory of evolution they espouse. However, landscapes mature, as do ecosystems. By employing the word in an ecological way, we can, perhaps, escape from always viewing the fossil record through evolution-tinted glasses.

The Ordovician spores are referred to as cryptospores because they have some unusual features. Wellman lists seven reasons why the spores should be associated with bryophytes in general and liverworts in particular. Interestingly, the research team found fossilised spores from five different types of liverwort, which is evidence of diversification:

"Spores of liverworts are very simple and are called cryptospores," Dr Rubinstein told the BBC. "The cryptospores that we describe are the earliest to date." These spores, dating from between 473 and 471 million years ago, come from plants belonging to five different genera - groups of species. "That shows plants had already begun to diversify, meaning they must have colonised land earlier than our dated samples," said Dr Rubinstein.

To appreciate the ecological significance of the discovery, we need to remind ourselves of the inhospitable environments that existed in the Ordovician. What land plants could conceivably have survived, let alone prosper, when faced with such arid terrains?

"Colonization of the land by plants presumably occurred in a step-wise fashion starting during the Early Paleozoic with plants at a bryophyte, most likely liverwort, grade of organization. It resulted in acceleration of weathering processes and in the formation of modern terrestrial environments, including structured soils and complex microbial communities; it also profoundly affected carbon cycling, changed the atmosphere composition and irreversibly altered climates."

In such environments, plants lacking stems and roots have significant advantages. Liverworts were able to colonise the land. The lack of a good soil is no disadvantage to a plant without roots, although they do have structures to anchor them to the ground and to absorb water. Their ability to survive both droughts (desiccation up to 90% of water content) and water-logged periods is an asset. The complex process of photosynthesis allows these plants to gain whet they needed to survive and multiply. "Bryophytes assist in the stabilisation of soil crust by colonising bare ground and rocks, and are essential in nutrient recycling, biomass production, and carbon fixing." (source here)

On ecological grounds, the plants that grew in the Ordovician were ideally suited to initiating the colonisation process. They were not there because they were primitive (because there are plenty of complexities if we look for them) but because they were pioneers in the colonisation process. Furthermore, although there is evidence of diversification, the message we need to take home is one of stasis. Having established diversity, the authors of the research paper are constrained to comment that this same diversity is apparent at higher stratigraphical levels. It would appear that diversification was accompanied by stasis. This is not a story of macroevolutionary transformation, but of variations within a basic type. Today there are over 6,000 liverwort species: there is plenty of evidence for diversification, but all of it is within the Liverwort group.

"The assemblage described here includes five cryptospore genera. Both from morphological and systematic points of view, this Dapingian assemblage is not different from younger cryptospore occurrences, including Aeronian (Early Silurian, c. 439-436 Ma) assemblages. This seems to indicate that the evolutionary rate of the earliest embryophytes was extremely low, or that selective pressures did not act on the morphology of propagules."

Early Middle Ordovician evidence for land plants in Argentina (eastern Gondwana)
C. V. Rubinstein, P. Gerrienne, G. S. De La Puente, R. A. Astini, P. Steemans.
New Phytologist (October 2010) 188(2): 365-369 | doi: 10.1111/j.1469-8137.2010.03433.x

Summary: The advent of embryophytes (land plants) is among the most important evolutionary breakthroughs in Earth history. It irreversibly changed climates and biogeochemical processes on a global scale; it allowed all eukaryotic terrestrial life to evolve and to invade nearly all continental environments. Before this work, the earliest unequivocal embryophyte traces were late Darriwilian (late Middle Ordovician; c. 463-461 million yr ago (Ma)) cryptospores from Saudi Arabia and from the Czech Republic (western Gondwana). Here, we processed Dapingian (early Middle Ordovician, c. 473-471 Ma) palynological samples from Argentina (eastern Gondwana). We discovered a diverse cryptospore assemblage, including naked and envelope-enclosed monads and tetrads, representing five genera. [snip]

See also:

Wellman, C.H. The invasion of the land by plants: when and where? New Phytologist, (October 2010) 188(2): 306-309 | DOI: 10.1111/j.1469-8137.2010.03471.x

Walker, M. Fossils of earliest land plants discovered in Argentina, BBC News, 12 October 2010.

On Thursday, October 28th the world's largest museum of African American history will host a debate exploring the impact of Darwin's theory on eugenics and scientific racism. Organized by the Charles H. Wright Museum of African American History in Detroit, "Darwin's Legacy: Scientific Breakthrough or Breakdown?" is co-sponsored by Discovery Institute and WLQV-AM 1500. Moderator for the event is author and broadcast journalist Edward Foxworth.

More...

According to ENV...Mark A. Chancey claims ID "originated within certain religious circles and has credibility only within those same circles - mostly theologically conservative Christian groups that find aspects of evolutionary theory threatening." Whatever else may be said of his characterizations, the statement above is surely bad history and not an accurate reflection of the development of modern ID.

More...

An Intelligent Design lecture/discussion group will meet at the University of New Mexico in Albuquerque.

Tuesday, October 19th

7-9 PM

University of New Mexico Law School

Room 2405

More for topics...

by Denyse O'Leary
ARN correspondent

In "Looking for Life in the Multiverse: Universes with different physical laws might still be habitable" Scientific American Magazine (December 16, 2009) By Alejandro Jenkins and Gilad Perez make clear what is and is not accepted in science (as they understand it) and why:

The laws of physics-and in particular the constants of nature that enter into those laws, such as the strengths of the fundamental forces-might therefore seem finely tuned to make our existence possible. Short of invoking a supernatural explanation, which would be by definition outside the scope of science, a number of physicists and cosmologists began in the1970s to try solving the puzzle by hypothesizing that our universe is just one of many existing universes, each with its own laws. According to this"anthropic" reasoning, we might just occupy the rare universe where the right conditions happen to have come together to make life possible. Amazingly, the prevailing theory in modern cosmology, which emerged in the1980s, suggests that such "parallel universes" may really exist-in fact, that a multitude of universes would incessantly pop out of a primordial vacuum the way ours did in the big bang. Our universe would be but one of many pocket universes within a wider expanse called the multiverse. In the overwhelming majority of those universes, the laws of physics might not allow the formation of matter as we know it or of galaxies, stars, planets and life. But given the sheer number of possibilities, nature would have had a good chance to get the "right" set of laws at least once. Our recent studies, however, suggest that some of these other universes-assuming they exist-may not be so inhospitable after all. Remarkably, we have found examples of alternative values of the fundamental constants, and thus of alternative sets of physical laws, that might still lead to very interesting worlds and perhaps to life. The basic idea is to change one aspect of the laws of nature and then make compensatory changes to other aspects.

Our work did not address the most serious fine-tuning problem in theoretical physics: the smallness of the "cosmological constant," thanks to which our universe neither recollapsed into nothingness a fraction of a second after the big bang, nor was ripped part by an exponentially accelerating expansion. Nevertheless, the examples of alternative, potentially habitable universes raise interesting questions and motivate further research into how unique our own universe might be.

Well, the supernatural may be "outside the scope of science," but universes whose existence is not demonstrated, which are imagined principally to get out of a jam with the evidence from this universe, are reasonably doubted, despite thought experiments. The tentative tone here is well justified. It should be used more often.

See other multiverse and fine tuning stories:

Cosmology: If you needn't worry about paying the rent Friday, you can worry about this stuff

Cosmology: Science's leader in things that don't make sense

Cosmology: Crisis of the month: gravitation

Cosmology: Multiverse - getting comfortable with a zillion of everything that is unique.

Cosmology: I seem to have yanked particle physicist Lawrence Krauss's chain

Cosmology: Wow. It takes guts to wage war with Stephen Hawking. He appeared in Star Trek

Cosmology: Arguments against flatness (plus exposing sloppy science writing)

Cosmology: If the universe has free will, where do I go to file a claim for damages?

Anr2

by Denyse O'Leary
ARN correspondent

A recent news story featured an astronomer whose personal feelings about the chances for life on a recently discovered planet orbiting a star other than our sun were 100%:

Personally, given the ubiquity and propensity of life to flourish wherever it can, I would say, my own personal feeling is that the chances of life on this planet are 100 percent," said Steven Vogt, a professor of astronomy and astrophysics at the University of California, Santa Cruz, during a press briefing today.

"I have almost no doubt about it.”

He might have done with a few doubts about planet Gliese 581 g, which has a 37-day orbit around a dim, red dwarf star. The
latest story is that other astronomers can’t establish that Gliese exists.

Two weeks after one team of astronomers announced finding the habitable planet Gliese 581 g, another team says it can find no evidence of the world in its data.

Last month, a team of astronomers announced the discovery of the first alien world that could host life on its surface. Now a second team can find no evidence of the planet, casting doubt on its existence.

[ ... ]

But it might be too early to claim a definitive detection. A second team of astronomers have looked for signals of Gliese 581 g in their own data and failed to find it.

"We easily recover the four previously announced planets, "b", "c", "d", and "e". However, we do not see any evidence for a fifth planet in an orbit of 37 days," says Francesco Pepe of the Geneva Observatory in Switzerland. He presented the results on Monday at an International Astronomical Union symposium in Turin, Italy.

Although the Geneva team cannot find evidence for the new planet, they cannot exclude the possibility that Gleise 581 g exists. "We are not trying to prove the nonexistence of a planet," Pepe says. "It's really difficult to prove that something does not exist. We are just saying we do not see a significant signal that is really different from noise."

- Rachel Courtland, "First life-friendly exoplanet may not exist", 1(3 October 2010)

Well, as we, and they, all know, one cannot prove that a physical thing really does not exist. One simply reaches the point where one considers its existence too improbable to spend more time looking.

If Gliese is not found, the episode will demonstrate one important thing: Many people badly need to believe in life on other planets, and many more people are eager to hear them tell about it. The legendary caution of science stands no chance against the onslaught of such yearnings.

See also Exoplanets: The recent pilgrimage to Darwin's shrine.

Does our solar system occupy a unique position in the universe or just an ordinary one?

Rare? Solar systems like ours are rare?

Astronomer argues that we can test whether Earth is fine-tuned as a science lab

Serious push to find more exoplanets

Exoplanets: Will intelligence be common or rare?

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

During the 1990s I had untold opportunities to witness the full exuberance of nature's rich offerings. My parents' house on the southwestern edge of Ecuador's capital Quito was set in a prime location for observing all manner of wildlife. And most memorable of all were the hummingbirds that frequented our garden attracted as they were to the blooming plants that had been strategically potted next to the outside walls of our living room. These veritable masters of flight, the smallest of warm blooded creatures on our planet, arrived with the sole purpose of extracting sweet nectar from the flowers we had laid before them. Their hovering maneuverability was their most striking attribute.

To date over 330 different species of hummingbird have been identified across the expanse of the American continent (1-3). And the mechanisms behind their supreme agility are being dissected out by the likes of UC Riverside biologist Doug Altshuler (1,4). Using revolving feeders filled with nectar and cameras that record minute positional adjustments relative to feeder rotation, Altshuler has uncovered one of the secrets behind these birds' exquisite capabilities: flexible rotating shoulder bones that allow them to hover while maintaining their bills firmly inside flowers (1,2). With little to no opportunity to perch during feeding, their wing anatomy is indispensable for survival (1). On average 'hummers' consume more than half their body weight in nectar extracted from as many as 1000 flowers each day (1). To sustain this extraordinary rate of consumption their berry-sized hearts must beat 600 times a minute during rest and almost double that during flight (1). This totals up to 4.5 billion times during their 12-17 year lifespan (4). A continuous feeding binge supplies them with the energy they need to beat their tiny wings a staggering 80-200 times per second (1,2).

In the mountain forests of Ecuador, not far from where my parents lived, there exists a species of hummer whose popular name, the swordbill, accurately describes the appearance of its feeding accoutrement (1,5). With its four inch beak the swordbill is able to feed on the nectar of the Datura plant (1,5). And it turns out that it is uniquely equipped for the job. Because Datura blossoms hang straight down, a four inch bill is what it takes to gorge on the effusions coming out of nectaries at the very base of the flower. But there is a trade-off. As the bird feeds, it is dusted with pollen that it carries to its next port of call (1).

Although hummers are built to feed on nectar, they cannot sustain themselves on sugar alone. They depend heavily on insects as a primary source of protein (3). It is little wonder then that bugs form 1/4 of their daily diets (1). With deadly accuracy hummers can pick out their prey mid-flight by opening their flexible bills to the widest capture position possible (1). And that is not the only way their bills are so refined for the functions they perform. Today eight thousand plant species depend on the hummer for pollination. Like a lock and key, each bill fits into a limited set of blossoms. The Purple-throated Carib even exhibits marked gender differences in bill length tailored as they are to feed on different species of the colorful Heliconia plant (1).

At nighttime hummers thwart the clutches of starvation by fluffing up their feathers to conserve heat and entering into a low energy sleep state called Torpor (3). By lowering their heart rates to a sluggish 36 beats per minute and their body temperatures from a comfortable 105 degrees Fahrenheit to the 'hypothermic threshold' of life, they barely manage to stay alive (1,3). The process is easily reversed however. And when day breaks, vital signs ramp up to normal in 20 minutes or less in readiness for another day of high cost flying (3).

Flight behaviors amongst hummers challenge even our most optimistic preconceptions of avian aerobatics. UC-Berkeley biologist-engineer Chris Clark has captured the steep death-defying 60 miles/h dive of the male Anna's on camera as they perform a carefully choreographed mating display (6). By taking high definition shots at 500 frames per second Clark estimates that g forces in the Anna's dive match those at which military fighter pilots black out (1). Males descend at such an angle and speed that their tail feathers vibrate at the appropriate acoustic frequency to woo female onlookers (6). When it comes to heroic feats, most hummer votaries will wax lyrical over the seasonal migrations of their feathered icons. Licensed 'banders' devote much time to the study of feeding and migration habits by crimping tiny uniquely-coded metal rings onto the hummers' toothpick-sized legs (7,8). And their work has brought the hummers' continent-wide peregrinations into sharp focus. Some fly as many as 6000 miles between North and Central America breeding in the temperate zones of the north and wintering in the warmer climes of the south (3). One species, the Ruby Throat, even endures an 18 hour, 500 mile long trek across the open waters of the Gulf of Mexico with no place to stop or feed, by storing the extra 2-3 grams of fat it needs to make it across (3).

The hummer story tells of irreducible complexity at key levels of functionality. Anatomically these birds require not only a unique hovering system and long beaks but also a heart that can keep up with their voracious appetites. And the exacting nature of their specific behaviors leaves little room for evolution's undirected mutational 'potshots'. Species like the Ruby Throat, for example, need to binge on the grub that will get them through their sea-crossing expedition. But their food quota must be carefully regulated. Too little nourishment means not enough energy to make it across. Too much nourishment and they risk over-weighting themselves and plunging into the unrelenting waters below.

There is one hummer that is indelibly etched into my wish list of nature's must-sees- the Peruvian Spatuletail (9). The furious waving of its long tail feathers during courtship has recently been captured on camera (9). And like everything else in the hummer, these movements are made at neck-breaking speed (9). The Spatuletail waves the spoon-shaped spatules at the ends of its feathers while hopping on a twig 14 times a second (10). Awakened by such feats, my parents and I indulged in a little ecotourism by traveling down to the Maquipucunia nature reserve about 50 miles to the north of Quito in Ecuador (9). Even though we knew little about the birds that graced the hills of this unspoiled paradise, we were able to appreciate the numerous hummers as they flaunted their iridescent colors. The setting could not have been more visually arresting. And while we never made it down to Peru what we saw more than made up for that particular missed opportunity.

Further Reading

1. Hummingbirds: Magic In The Air, See PBS Nature Special at http://www.pbs.org/wnet/nature/episodes/hummingbirds-magic-in-the-air/introduction/5424/

2. Mike Klesius (2007) Hummingbirds: Flight Of Fancy, National Geographic, January 2007, See http://ngm.nationalgeographic.com/2007/01/hummingbirds/klesius-text/1

3. How do Hummingbirds survive cold nights? Hummingbirds and Torpor, See http://scienceblogs.com/grrlscientist/2006/04/hummingbirds_and_torpor.php

4. Biologist's Lab at UC Riverside Is a Hummingbird Health Spa, See http://newsroom.ucr.edu/news_item.html?action=page&id=2233

5. Mary O'Leary (2009) Local filmmaker captures hummingbirds for PBS, New Haven Register, December 27th, 2009, See http://www.nhregister.com/articles/2009/12/27/news/new_haven/doc4b36ce70697f1930415349.txt

6. Robert Sanders (2008) Anna's hummingbird chirps with its tail, http://berkeley.edu/news/media/releases/2008/01/30_hummingbird.shtml

7. Like Banding A Toothpick! Talking With Sarah Driver, Hummingbird Bander, See http://www.learner.org/jnorth/tm/humm/HumBander_Sarah.html

8. Hummer/Bird Banding Research Collaborative (HBBRC) http://www.hbrcnet.org/index.htm

9. The Maquipucunia Reserve: http://maqui.myweb.uga.edu/

10. Matt Walker (2009) A Marvelous Hummingbird Display, BBC Earth News, 3rd November, 2009, http://news.bbc.co.uk/earth/hi/earth_news/newsid_8338000/8338728.stm

Review Of Programming of Life By Donald Johnson, ISBN-10: 0982355467
By Robert Deyes
ARN Correspondent

There are some science writers that quite simply have a knack for combining the detail of their subject of expertise with a talent for exposition that a wide audience can easily understand. Donald Johnson is one of them. After carefully defining the various types of information- functional, prescriptive and Shannon- that information theorists have set out in their realm of study, Johnson takes the reader on a tour of cellular gene expression by focusing on the digital code of DNA. Shannon information, which provides a mathematical measure of improbability without regard to functionality does not help us in the description of life since the digital code of DNA is rich in what Johnson terms 'functional prescriptive information'.

While initiatives such as the Origin Of Life Prize have encouraged researchers to find non-super-naturalistic processes that might explain the origins of prescriptive information, no offerings to-date have withstood the test of scientific scrutiny. Indeed all known cases of such information invariably point to the work of a mind. Johnson emphasizes the relevance of probability in his espousal of this inference- the simplest form of life was found to be 10exp80,000 times more likely of having a mindful than a non-mindful source.

Johnson repeatedly stresses how the information content of DNA is analogous to the information carried on a computer disk drive.Within such a schema, each of the enzymes that decode the information can be seen as individual computers that bring meaning to the code through the RNA that is transcribed and the proteins that are translated. 23,000 genes make up the human genome. And the multi-functional nature of these genes in self evident in the way that RNAs are differentially spliced and glued together.

Johnson's perspective packs a might punch on the evolutionary edifice. Computer simulations and evolutionary algorithms such as MeThinksItIsLikeAWeasel and AVIDA have failed to show how evolution can generate prescriptive information since pre-specified targets, unrealistic protection of replication instructions and unrealistic energy rewards abound in each of these systems.

While the battle over the categorization of junk DNA rages on amongst biologists, Johnson gives us a succinct and well-buttressed view on the subject: "Researchers are discovering that what has been dismissed as evolution's relics are actually vital for life". There is no evidence that new prescriptive information can be built up by genetic rearrangements such as transposition, inversion, duplication or point mutation. We can therefore understand Lynn Margulis' reference to the Darwinian claim as a `half truth' grounded in religious ferocity. This half truth forms the foundation for Johnson's final attack as he considers the merits of irreducible complexity and Craig Venter's recently produced artificial genome. Rather than showing how an organism could arise from scratch, Venter's enterprising achievement revealed the need for careful engineering of existing parts into a form that could be introduced into an existing organism.

Johnson's writing style is captivating. The extensive range of resources he draws from only serves to build confidence in the factual accuracy of his case. What a terrific read. Sheer brilliance.

by Denyse O'Leary
ARN correspondent

How do we know?

"Personally, given the ubiquity and propensity of life to flourish wherever it can, I would say, my own personal feeling is that the chances of life on this planet are 100 percent," said Steven Vogt, a professor of astronomy and astrophysics at the University of California, Santa Cruz, during a press briefing today.

"I have almost no doubt about it."

Well, that settles it, I guess.

James M. Kushiner points out, at Mere Comments blog, re Odds of Life on Nearby Planet '100 Percent,' Astronomer Says":

Did you hear about the astronomer, who said, get this, that the odds of life on nearby planet are 100 Percent? What was he thinking? What do astronomers know about biological life, and, besides, if the odds are 100 percent, then there are no odds--at least if I go to Arlington Race Track and find a horse that has a 100 percent chance of winning, they probably won't be taking bets on him. No odds there.

[ ... ]

I am not saying this planet could not support life. I am just wondering what are the chances that any given astronomer would peg a planet with so many unknowns or uncertainties with a probability of having life on it at 100 percent? Of course, if a news story is in play with a possible headline, I'd up those chances considerably, whatever they are.

If you want to read science, don't read the news.

Read more here.

Kushiner is editor of the science and popular culture mag Salvo, which publishes my Deprogram column, and many authors you recognize.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

by Denyse O'Leary
ARN correspondent

In, "Document Sheds Light on Investigation at Harvard (Chronicle Review, August 19, 2010)," Tom Bartlett reports that Harvard has told evolutionary psychologist Marc D. Hauser to explain issues around a few of his journal articles:

The experiment tested the ability of rhesus monkeys to recognize sound patterns. Researchers played a series of three tones (in a pattern like A-B-A) over a sound system. After establishing the pattern, they would vary it (for instance, A-B-B ) and see whether the monkeys were aware of the change. If a monkey looked at the speaker, this was taken as an indication that a difference was noticed.

The method has been used in experiments on primates and human infants. Mr. Hauser has long worked on studies that seemed to show that primates, like rhesus monkeys or cotton-top tamarins, can recognize patterns as well as human infants do. Such pattern recognition is thought to be a component of language acquisition.

Researchers watched videotapes of the experiments and "coded" the results, meaning that they wrote down how the monkeys reacted. As was common practice, two researchers independently coded the results so that their findings could later be compared to eliminate errors or bias.

According to the document that was provided to The Chronicle, the experiment in question was coded by Mr. Hauser and a research assistant in his laboratory. A second research assistant was asked by Mr. Hauser to analyze the results. When the second research assistant analyzed the first research assistant's codes, he found that the monkeys didn't seem to notice the change in pattern. In fact, they looked at the speaker more often when the pattern was the same. In other words, the experiment was a bust.

But Mr. Hauser's coding showed something else entirely: He found that the monkeys did notice the change in pattern—and, according to his numbers, the results were statistically significant. If his coding was right, the experiment was a big success.

Well, the long and short of it is that no one in Hauser's own lab could replicate his results.

The research that was the catalyst for the inquiry ended up being tabled, but only after additional problems were found with the data. In a statement to Harvard officials in 2007, the research assistant who instigated what became a revolt among junior members of the lab, outlined his larger concerns: "The most disconcerting part of the whole experience to me was the feeling that Marc was using his position of authority to force us to accept sloppy (at best) science."

Hauser was found to be solely responsible for the discrepancies, and as of the date of the Chronicle Review article, was on leave.

The whole story is testimony to the sheer need some have to prove that apes and monkeys are just fuzzy people or we are just naked apes. Life, whatever it is, is not that simple.

According to Hauser's Edge bio,

MARC D. HAUSER, an evolutionary psychologist and biologist, is Harvard College Professor, Professor of Psychology and Program in Neurosciences, and Director of Primate Cognitive Neuroscience Laboratory. He is the author of The Evolution of Communication, Wild Minds: What Animals Think, and Moral Minds: How Nature Designed Our Universal Sense of Right and Wrong.

[ ... ]

Along with Irv Devore, he teaches the Evolution of Human Behavior class, a Core Course at Harvard with 500 undergraduate students. The interdisciplinary course, "Science B29" (nickname: "The Sex Course"), has been running for 30 years, was started by Devore and Robert Trivers, and is the second most popular course on campus, behind "Econ 10". Section teachers over the years comprise a who's who of leading thinkers and include people such as John Tooby and Leda Cosmides, and Sarah B. Hrdy. In 1997-98, he sponsored a trial run of "Edge University" in which the students in Science B29 received Edge mailing as part of required reading in the course.

Re his book, Wild Minds: What Animals Think, it was what humans think that proved his undoing.

See also:

Wisdom from your local zoo

Evolutionary psychology: All wrong all the time

Humans are unique - get used to it, or get therapy. Do NOT get a chimpanzee

Dogs more like humans than chimpanzees are?

"Loving" chimpanzee eats its victims alive, new research shows

New assessment of ape language skills is dramatically scaled back

A defense of Apes r us - and insider look at the pygmy chimpanzee enthusiasts

Apes R Not Us, and we have to get used to it

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

The archetypal image of Neanderthals has been one that reinforced the Darwinian story of human evolution. A Washington Post story puts it like this: "Early study of Neanderthals described them as very hairy, brutish, unable to talk or walk like more-modern humans." Although things have changed slowly, media presentations have continued to create an impression that does not differ much from this description. However, the evidence for their humanity has accumulated rather rapidly in recent years, and the past month has seen two significant additions to the literature. A Wired Science report introduces one of these studies like this:

"For decades, Neanderthal was cultural shorthand for primitive. Our closest non-living relatives were caricatured as lumbering, slope-browed simpletons unable to keep pace with nimble, quick-witted Homo sapiens. However, anthropologists have found evidence in recent years suggesting considerable Neanderthal sophistication, and not only in tool-making and hunting, but in their ability to feel [i.e. to show compassion]."

It is time to wear the t-shirt (Source here)

The first paper is concerned with the role of emotions in social relationships and re-appraises the archaeological record of Neanderthals and other Palaeolithic peoples. A summary is provided by Penny Spikins in an interview with Wired.

"We look in the archaeological record for evidence of individuals who were sick, and not able to care for themselves. We see that in early Homo, and by the time we get to Neanderthals, that kind of record becomes much more extensive. Take the "Old Man of Shanidar". He had had degenerative deformities in the base of his legs, would have had difficulty walking, and had a crushing injury to his cranium, so he was probably blind in his left eye. The bones show those injuries occurred when he was adolescent, and he lived to 40. He was probably looked after for 25 to 30 years, which implies that it wasn't just one person looking after him, but several. Most of our Neanderthal skeletons show some evidence of having been looked after for their injuries. And in the age of Neanderthals, you also start to see evidence of deliberate burials and funerary rites. That means a shared feeling."

The other study is from Julien Riel-Salvatore, who has come to realise that the explanations given to evidences of Neanderthal technology and cultural artefacts is flawed. It has been said that Neanderthals gained 'modern' tools and ornaments through contact with groups of migrating Homo sapiens. The thinking was that Neanderthals could not have done it on their own - they lacked creativity. However, by studying a group of Neanderthals that lived separately from Homo sapiens, the picture changes dramatically.

The findings by anthropologist Julien Riel-Salvatore challenge a half-century of conventional wisdom maintaining that Neanderthals were thick-skulled, primitive 'cavemen' overrun and outcompeted by more advanced modern humans arriving in Europe from Africa. "Basically, I am rehabilitating Neanderthals," said Riel-Salvatore, assistant professor of anthropology at UC Denver. "They were far more resourceful than we have given them credit for."

The research has involved an analysis of Uluzzian archaeological sites throughout southern Italy, and Riel-Salvatore has come to the conclusion that the inhabitants responsible for the artefacts were Neanderthals who developed their own unique blend of "projectile points, ochre, bone tools, ornaments".

Such innovations are not traditionally associated with Neanderthals, strongly suggesting that they evolved independently, possibly due to dramatic changes in climate. More importantly, they emerged in an area geographically separated from modern humans. "My conclusion is that if the Uluzzian is a Neanderthal culture it suggests that contacts with modern humans are not necessary to explain the origin of this new behavior. This stands in contrast to the ideas of the past 50 years that Neanderthals had to be acculturated to humans to come up with this technology," he said. "When we show Neanderthals could innovate on their own it casts them in a new light. It 'humanizes' them if you will."

The picture that is emerging, reinforced and validated by the newly reported research, is that Neanderthals are somewhat different, but nevertheless equal. The evolutionary story is misleading and it needs to be discarded. The comments of Riel-Salvatore are spot on:

"The fact that Neanderthals could adapt to new conditions and innovate shows they are culturally similar to us," he said. "Biologically they are also similar. I believe they were a subspecies of human but not a different species." [. . .] "It is likely that Neanderthals were absorbed by modern humans," he said. "My research suggests that they were a different kind of human, but humans nonetheless. We are more brothers than distant cousins."

A previous blog had the title: Neandertals are part of the human family. Other blogs in this series carried similar messages. Burying the view that Neanderthals were half-wits, Darwinist thinking on the origin of religion, The cognitive skills of Stone Age Man, Images of evolution as secular icons, Walks like a man, talks like a man - is it a man?, and Rethinking Neanderthals. If we are prepared to follow the science, we must move on in our understanding of Neanderthals!

From Homininity to Humanity: Compassion from the Earliest Archaics to Modern Humans
Spikins, P.A.; Rutherford, H.E.; Needham, A.P.
Time and Mind, 3(3), November 2010, pp. 303-325 | DOI: 10.2752/175169610X12754030955977

Abstract: We are increasingly aware of the role of emotions and emotional construction in social relationships. However, despite their significance, there are few constructs or theoretical approaches to the evolution of emotions that can be related to the prehistoric archaeological record. Whilst we frequently discuss how archaic humans might have thought, how they felt might seem to be beyond the realm of academic inquiry. In this paper we aim to open up the debate into the construction of emotion in early prehistory by proposing key stages in the emotional motivation to help others; the feeling of compassion, in human evolution. We review existing literature on compassion and highlight what appear to be particularly significant thresholds in the development of compassion for human social relationships and the evolution of the human mind.

A Niche Construction Perspective on the Middle-Upper Paleolithic Transition in Italy
Julien Riel-Salvatore
Journal of Archaeological Method and Theory, published online 19 August 2010 | DOI 10.1007/s10816-010-9093-9

Abstract: This paper presents an overview of the Middle-Upper Paleolithic transition in Italy in light of recent research on the Uluzzian technocomplex and on the paleoecological context of the transition. Drawing on the realization that human niche construction can be documented in the pre-agricultural archaeological record, niche construction theory is used as a conceptual framework to tie together facets of the behavioral, biological, and ecological dimensions of the transition interval into formal models of their interaction over time and in diverse contexts. Ultimately, this effort shows how foragers of the transitional interval in the Italian peninsula were active agents in shaping their evolutionary history, with consequences of some adaptive systems being felt only much later and directing the forces responsible for the ultimate disappearance of the Mousterian and Uluzzian technocomplexes in favor of the proto-Aurignacian industry, the exact nature of which clearly appears to vary on a regional level.

See also:

Neanderthals more advanced than previously thought, EurekAlert, (September 21, 2010)

Drosophila melanogaster is a model organism for the study of genetics and some laboratory populations have been bred for different life-history traits over the course of 30 years. Professor Michael Rose, of UC Irvine, began breeding flies with accelerated development in 1991 (600 generations ago). Doctoral student Molly Burke compared the experimental flies with a control group on a genome-wide basis. This is significant because it is the first time such a study of a sexually reproducing species has been done. Burke examined specific genes and also obtained "whole-genome resequencing data from Drosophila populations that have undergone 600 generations of laboratory selection for accelerated development." The results are noteworthy on several counts:

"For decades, most researchers have assumed that sexual species evolve the same way single-cell bacteria do: A genetic mutation sweeps through a population and quickly becomes "fixated" on a particular portion of DNA. But the UCI work shows that when sex is involved, it's far more complicated. "This research really upends the dominant paradigm about how species evolve," said ecology and evolutionary biology professor Anthony Long, the primary investigator.

"

Knowing the genome sequence of Drosophila has opened new avenues of research (Source here)

The researchers were looking for the fixation of positive mutations within the genome and within the whole population. This is referred to using the term "selection sweep". When it occurs, the new mutation at a base pair (a novel single nucleotide polymorphism or SNP) not only experiences replication to be transmitted to the descendants of the organism, but the gene pool of variation is effectively swept clean as the new mutation becomes dominant in the whole population. However, such sweeping was conspicuous by its absence.

"Recent research on evolutionary genetics has focused on classic selective sweeps, which are evolutionary processes involving the fixation of newly arising beneficialmutations. In a recombining region, a selected sweep is expected to reduce heterozygosity at SNPs flanking the selected site. [. . .] Notably, we observe no location in the genome where heterozygosity is reduced to anywhere near zero, and this lack of evidence for a classic sweep is a feature of the data regardless of window size."

The paper considers a range of possible explanations for the evidence obtained. First: "Classic sweeps may be occurring, but have had insufficient time to reach fixation." Second: "selection in these lines may generally act on standing variation, and not new mutations." Third, "selection coefficients associated with newly arising mutations are not static but in fact decrease over time." No conclusion is reached regarding these various options.

"Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles. This is notable because in wild populations we expect the strength of natural selection to be less intense and the environment unlikely to remain constant for ~600 generations. Consequently, the probability of fixation in wild populations should be even lower than its likelihood in these experiments. This suggests that selection does not readily expunge genetic variation in sexual populations, a finding which in turn should motivate efforts to discover why this is seemingly the case."

This empirical work is worth noting on two counts. First, we are here considering a mechanism that is central to Darwinian evolution. Positive natural selection of hereditable variation is the key (we are informed) to understanding how descent with modification occurs. However, the first set of empirical data relating to a sexually reproducing species does not confirm that modification works this way. This is why Long's comment is worth repeating: "This research really upends the dominant paradigm about how species evolve". Many scientists have long suspected that the Darwinian mechanisms are inadequate to account for large-scale transformation - these research findings provide empirical support for such doubts.

The other reason for taking an interest in this research is that the Darwinian paradigm has been widely used in the development of drugs for medical use. Whereas the classical view is that genes have specific functions, the new research supports the growing body of evidence that the norm is for genes to have pleiotropic effects. A novel SNP can then be expected to have not one, but many, effects. This has been underplayed by researchers of a darwinian persuasion.

"Based on that flawed paradigm, Rose noted, drugs have been developed to treat diabetes, heart disease and other maladies, some with serious side effects. He said those side effects probably occur because researchers were targeting single genes, rather than the hundreds of possible gene groups like those Burke found in the flies. Most people don't think of flies as close relatives, but the UCI team said previous research had established that humans and other mammals share 70 percent of the same genes as the tiny, banana-eating insect known as Drosophila melanogaster."

Genome-wide analysis of a long-term evolution experiment with Drosophila
Molly K. Burke, Joseph P. Dunham, Parvin Shahrestani, Kevin R. Thornton, Michael R. Rose and Anthony D. Long.
Nature, 467, 587-590, (30 September 2010) | doi: 10.1038/nature09352 (preprint)

Experimental evolution systems allow the genomic study of adaptation, and so far this has been done primarily in asexual systems with small genomes, such as bacteria and yeast. Here we present whole-genome resequencing data from Drosophila melanogaster populations that have experienced over 600 generations of laboratory selection for accelerated development. Flies in these selected populations develop from egg to adult ~20% faster than flies of ancestral control populations, and have evolved a number of other correlated phenotypes. On the basis of 688,520 intermediate-frequency, high-quality single nucleotide polymorphisms, we identify several dozen genomic regions that show strong allele frequency differentiation between a pooled sample of five replicate populations selected for accelerated development and pooled controls. On the basis of resequencing data from a single replicate population with accelerated development, as well as single nucleotide polymorphism data from individual flies from each replicate population, we infer little allele frequency differentiation between replicate populations within a selection treatment. Signatures of selection are qualitatively different than what has been observed in asexual species; in our sexual populations, adaptation is not associated with 'classic' sweeps whereby newly arising, unconditionally advantageous mutations become fixed. More parsimonious explanations include 'incomplete' sweep models, in which mutations have not had enough time to fix, and 'soft' sweep models, in which selection acts on pre-existing, common genetic variants. We conclude that, at least for life history characters such as development time, unconditionally advantageous alleles rarely arise, are associated with small net fitness gains or cannot fix because selection coefficients change over time.

See also:

Scientists Decode Genomes of Precocious Fruit Flies, ScienceDaily (September 19, 2010)

by Denyse O'Leary
ARN correspondent

Conventional, and fairly obvious, wisdom would suggest that the bear avoids being noticed by its prey by blending in with the landscape and moving through the snow on silent feet. Evolving that way should be easy enough - the colour gene drops out, and ...

We readily assume that the prey is on land, casting a wary eye around. Not necessarily. Some remarkable BBC footage suggests it may not be so simple:

Here, you will hear the bear stomping and see it clearly visible above clear ice - as it would be to a seal approaching a blowhole. Presumably, the seal - apprised of an unexpected caller - goes to another of its many blowholes. But once the bear sits down to wait quietly at one ... which one is it? The bear, observed, is apparently lucky one time in ten, by invisible patience alone. I don't see that anything would change if the bear was green or purple or ...

Is it possible that white coats are favored because they are less conspicuous to other bears, who tend to be crabby and territorial much of the time?

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

by Denyse O'Leary
ARN correspondent

Okay, pass on the zinger sauce. There's no insurance against head explosions.

I will be speaking at the God and Evolution event at Biola University in Los Angeles, October 16, 2010, on "Catholics and Evolution", from 10:50 - 11:15 am. They want $25 but the event lasts from 9:00 a.m. to 3:00 p.m, seems to include lunch, and a free copy of the book in which I have a chapter, God and Evolution.

Here are the details:

God And Evolution:

Protestants, Catholics, and Jews Explore Darwin's Challenge to Faith
with Marvin Olasky, Ph.D., Jonathan Wells, Ph.D., Ph.D., Jay Richards, Ph.D., Denyse O'Leary, John West, Ph.D., David Klinghoffer, Casey Luskin, J.D., Craig J. Hazen, Ph.D., John Bloom, Ph.D., Ph.D.

Click Here for more details & to RSVP now!

Can you believe in God and evolution at the same time? What is "theistic" evolution, and how consistent is it with traditional theism? What challenges does Darwin's theory pose for Protestants, Catholics, and Jews? Is it "anti-science" to question Darwinian theory? Explore these questions and more at this upcoming conference at Biola University.

Sponsored by the Discovery Institute and Biola's Master of Arts in Science and Religion.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

As reported in Inspire Magazine, Professor Michael Behe, a key figure in the Intelligent Design (ID) movement, will challenge his critics in a lecture tour of the UK in November.

Prof Behe is one of an increasing number of scientists who believe that modern biochemical evidence undermines the basis of Darwinian evolution.

The author of two ground-breaking books on ID - Darwin's Black Box (1996) and The Edge of Evolution (2007) - Behe's theory of irreducible complexity has drawn attacks from many neo-Darwinists, but not one of them has been able to refute it.

As Behe himself writes, in the years since the publication of 'Darwin's Black Box', "the As Behe himself writes, in the years since the publication of 'Darwin's Black Box', "the scientific argument for design is stronger than ever. Despite the enormous progress of biochemistry in the intervening years...despite implacable opposition from some scientists at the highest levels, the book's argument for design stands … there is very little of the original text I would change if I wrote it today.

More...

Politically Incorrect Scientist - How the Co-Founder of the Theory of Evolution by Natural Selection Advocated Intelligent Design

Alfred Russel Wallace, co-founder of the theory of evolution by natural selection, was second only to Charles Darwin as the 19th century's most noted English naturalist.

More...

In ENV...On Thursday, September 23, 2010, following a showing of the film Darwin's Dilemma, we presented a program of short talks in the Hughes-Trigg Theatre at Southern Methodist University (SMU). We argued that the neo-Darwinian theory of evolution has not solved these related problems:

- The origin of novel protein folds (talk by Axe)
- The origin of anatomical novelties (talk by Sternberg)
- The origin of animal body plans (talks by Nelson and Wells)

SMU biology lecturer John Wise attended the event - or so it appears, because he wrote a long "reply" to both the movie and our presentations, and cites our handout distributed at the information table. Wise did not ask any questions during the Q & A, however, or interact with any of us during our visit. Over the weekend (September 25-26), he then posted his comments at his webpage.

We put "reply" within quotation marks because Wise's page comprises such a rambling pastiche of assertions - some mutually contradictory, others irrelevant, or simply non-sequiturs - that it is difficult to sort out what he is actually arguing.

More...

Darwinian "triggers to persuasion and captivation" read more like the seven deadly sins.

by Denyse O'Leary
ARN correspondent

From my recent MercatorNet column:

The Darwinian world of brand marketing

We all know what evolutionary psychology (EP) has meant for sociology, psychology, and religious anthropology: a serious effort to explain human behaviour in terms of ape behaviour or "hardwired" Stone Age genes. For example, you get your selfish genes from your mother, so it's her fault if you don't visit her...

The EP academics, however pernicious their ideas, are doubtless just trying to understand. But what happens when their theories hit the business world? Fascinate: Your 7 Triggers to Persuasion and Captivation by Sally Hogshead (Harper Business, 2010) gives us a glimpse of the Darwinian universe, as opposed to the Judeo-Christian one.

Hogshead is a brand marketing specialist. She helps executives persuade us to pay more for a brand than for a reliable service. Her special theory, gathered from research studies of apes and brain scans, is that the best strategy is "fascinating" people, and she has identified seven triggers for the spells a perceptive marketer can cast on them: lust, mystique, alarm, prestige, power, vice, and trust.

This list vaguely echoes the seven deadly sins, except for the last. But caution! Here, trust is not an intuition about how the universe really works; it is manipulative. We are told, "trust doesn't demand a moral absolute - only absolute consistency." (p. 175)

Hogshead begins by disposing of free will. (MercatorNet, 30 September 2010) And she'll end by disposing of your bank account if you don't look sharp.

For example,

Still more news from the world of privilege: "Not so long ago, the height of epicurean indulgence was a gold box filled with Godiva chocolates ... Then, in an effort to expand, in 1999 Godiva made a fateful decision to distribute in mass retailers such as Barnes and Noble. The chocolates, which for the first time now included preservatives, were no longer a treat to be craved and desired. Now you could buy the gold box in strip malls. (Strip malls!)" (p. 79)

Huh? Does this writer really not know that millions of her fellow Americans crave the goods of strip malls in vain?

Read more here.

So tell me again, Uncle Doddy: Given the stats, how does sin promote survival - for anyone but the rackets downtown?

Denyse O'Leary is co-author of The Spiritual Brain.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

The Michael Reiss saga should not be quickly forgotten. His enforced resignation as the Royal Society's Director of Education in September 2008 was a blot on the history of the Royal Society (see here and here). Yet, after two years, few changes are apparent: Reiss continues to publish his "worldview" perspective on handling creationism in science education (see here) and Royal Society Fellows have continued to talk about irresolvable conflicts at the science/religion interface. It is encouraging, therefore, to find Sylvia Baker formulating a coherent analysis of the conflict and proposing a research agenda to inform future discussion of the issues.

"The controversy, resulting as it did in such serious consequences, raises many issues and concerns. This article will seek to address three of them. First will be considered the subject of the controversy, the teaching of creationism in science classes, second, the status and influence of such bodies as the Royal Society within the science community of the United Kingdom, and third, the question of to what extent the end result was obtained, not by impartial considerations, but rather by an atheistic agenda."

The Purported "NOMA Model" of Science and Religion (Source here)

Fundamental to the controversy is the question: "Is creationism science?" Both the Royal Society and Professor Reiss have declared that evolution is about science and creationism is about religion. They advocate a sphere sovereignty position, also known as NOMA (Stephen Jay Gould's Non-Overlapping MAgisteria). But Reiss recognises that creationism does not accept this position. Creationists have a different worldview, where it makes perfect sense to invoke intelligent design and to say that God's miraculous activity is a necessary part of any explanation of origins. This clash of worldviews is described by Baker in this way:

"The modern creationist movement itself takes a particular approach to the philosophy of science and the influence of world views on the question of origins, as exemplified by publications such as Nancy Pearcey's major work Total Truth: liberating Christianity from its cultural captivity. Schoolchildren who have been influenced by this approach may well have been taught in their homes and churches or mosques that both creation and evolution are essentially philosophical world-view frameworks that operate at the intersection of religion and science."

NOMA has not fared well under the scrutiny of philosophers. The main advocates today are scientists: mostly, but not exclusively, of an atheist persuasion. Baker quotes Professor Steve Fuller sympathetically:

"All theories with the grand explanatory aspirations of creationism or evolutionism are based on worldviews that people have believed for reasons other than their scientific payoff. [. . .] The problem here is one of practice, not principle. In particular, there is nothing intrinsically un- or anti-scientific about creationist ideas. On the contrary, creationist assumptions, especially when God is understood as an intelligent designer, have deeply informed the history of the science that both theists and atheists continue to promote today."

One of the worst aspects of this controversy is that the critics of Reiss failed to base their arguments on any empirical evidence. Their hostility was philosophical and dogmatic. Reiss, however, was responding to evidence drawn from the classroom. Baker refers to three surveys: one of students being taught in independent and state-maintained schools and two others in Christian schools.

"The three studies, taken together, suggest that creationist beliefs among pupils lead to 'an easing of the human spirit', exactly as Astley first predicted (2005, p. 49) when the educational setting is coherent with the religious basis of the pupil's life but that the opposite is true when the setting is hostile and debate is not permitted. In both settings the pupils had been made aware that a theory of origins exists which eliminates the need for a Creator and which is held by the majority of modern scientists. It seems to be the educational setting, not the creationist beliefs themselves, which is leading to an anguished mental state for thousands of young people."

Returning to the issue of philosophical opposition to Reiss, a survey of members of the US National Academy of Sciences shows that 85% are atheists. One of Reiss's atheist critics said that 90% of Fellows of the Royal Society would agree with the criticisms. This suggests a further research agenda to Baker:

"What exactly do [the nation's scientists] believe on this issue and are their views accurately reflected in the pronouncements of such major bodies as the Royal Society? What are their religious beliefs and how do those beliefs relate to their view of what science is?"

Happily, others are saying similar things whilst coming from a different perspective. A current example is an article by Matthew Reisz with the title The dogma delusion (The Times Higher, 23 September 2010). Based on these considerations, Baker writes:

"it is possible that Michael Reiss was sacrificed on the altar of the god of scientific atheism. Journalist Melanie Phillips has no doubt about the matter:
'Totalitarian atheism has taken another scalp. Michael Reiss has been forced out - for daring to suggest that children should be taught to discuss alternative views and subject them to the scrutiny of empirical reasoning.' "

Though regrettable, the forced resignation of Michael Reiss may yet focus attention on matters of great public concern. What is science? Do the beliefs of scientists influence the way they define science? Is NOMA a tool contrived by people with vested interests to manage the interface between science and religion? Baker summarises the issues thus:

"The controversy has been seen to depend on definitions of science and creationism. At the same time, the question of who has the power to define what science is has been raised, as has the possibility that at root the problem is a clash of ideologies, a battle between atheism and religion carried out in the context of science."

Creationism in the classroom: a controversy with serious consequences
Sylvia Baker
Research in Education, Volume 83, Number 1, May 2010, pp. 78-88

First para: On 16 September 2008 the Revd Professor Michael Reiss resigned from his position as Director of Education at the Royal Society. The immediate context of his resignation was the furore created by the media in the wake of an address that he had given on Thursday 11 September 2008 in Liverpool, at the annual Festival of Science organised by the British Association for the Advancement of Science. The story seemed to be of universal interest, with several papers next day devoting full-page spreads to it, under large, eye-catching headings. For example, the Times (12 September 2008) headlined with 'Royal Society and the case for creationism: leading scientists at odds with Government over religious education', claiming that the Royal Society was supporting Professor Reiss in his 'heretical' views, while the Guardian's banner headline on the same day was 'Teach creationism, says top scientist'.

by Denyse O'Leary
ARN correspondent

Here and here, historian of Nazi Germany Richard Weikart responds to yet another whitewash of Darwinism's role in helping to create a particularly malignant type of racism, this time by Darwinist Michael Ruse:

Last November at a conference on Darwinism I conversed with a graduate student in philosophy who embraced Ruse's position on the evolution of ethics, which is not all that unusual among evolutionists. He told me he believed that morality is a biologically innate response shaped by evolutionary processes. It has no independent, objective, or universal existence. I pressed this graduate student, asking him how far he was willing to take his ethical relativism. Upon his affirmation that he subscribed to it completely, I asked him if he thought Hitler was morally evil. After explaining that he personally found Hitler's views repugnant, he admitted that he had no basis for condemning Hitler and finally he conceded, "Hitler was OK."

I doubt Ruse would be comfortable saying that Hitler was OK, because Ruse's (and Darwin's) political views are miles apart from Hitler's. However, Ruse's worldview (and Darwin's own) does not, as far as I can see, provide any objective basis for opposing or condemning Hitler (or Stalin or Mao).

Weikart is repeatedly accused of saying things he does not say, principally, one suspects because the things he does say and can demonstrate are so damning that the only alternatives are acknowledgement or obfuscation.

Here's an interview I did with Weikart on how he got interested in Darwin and Hitler anyway (not how you might think?).

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

by Denyse O'Leary
ARN correspondent

Here's physicist Tipler's view on Stephen Hawking's recent decision that God is not necessary:

In 1966, Stephen Hawking published his first - completely valid - proof for the existence of God. Over the next seven years, he followed this with even more powerful valid theorems proving God’s existence.

So how did Hawking, who successfully proved God's existence, remain an atheist? Simple. He simply denied that the assumptions he used in his proofs were true. As a matter of logic, if the assumptions in a proof are not true, then the conclusions need not be true. What assumptions did the young Hawking make? He assumed that the laws of physics, mainly Einstein's theory of gravity, were true. In the summary of his early research, namely his book The Large Scale Structure of Space-Time, Hawking wrote:

It seems to be a good principle that the prediction of [God] by a physical theory indicates that the theory has broken down, i.e. it no longer provides a correct description of observations.

Hawking then began working on quantum gravity, in hopes that God would be at last eliminated from the equations. Alas, it was not to be: God was even more prominent - and unavoidable - in quantum gravity than in Einstein's theory of gravity. In his latest book, The Grand Design, Hawking has pinned his hope of eliminating God on M-theory, a theory with no experimental support whatsoever, hence not a theory of physics at all. Nor has it been proven that M-theory is mathematically consistent. Nor has it been proven that God has been eliminated from M-theory. There are disquieting signs (for Hawking and company) that He is also unavoidable in M-theory, as He is in Einstein’s gravity, and in quantum gravity.

In spite of what the atheist press is telling you, it's looking bad for atheism today. And it is extraordinary the lengths an atheist like Hawking will go to avoid the obvious: God exists.

Tipler is an entertainingly nutty physicist, capable of making some sharp points. The thing to see here is that the new atheists do not need evidence. What they have is much more valuable: They are not officially classed by most people as a religious position, so they can simply impose their view on institutions they did not found, do not own, and negligibly pay for, if at all.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

by Denyse O'Leary
ARN correspondent

Here's a revealing PhysicsWorld paper on peer review:

After running the model with 1000 scientists over 500 time-steps, Thurner and Hanel find that even a small presence of rational or random referees can significantly reduce the quality of published papers. When just 10% of referees do not behave "correctly" the quality of accepted papers drops by one standard deviation. If the fractions of rational, random and correct referees are about 1/3 each, the quality selection aspect of peer review practically vanished altogether.

"Our message is clear: if it can not be guaranteed that the fraction of rational and random referees is confined to a very small number, the peer-review system will not perform much better than by accepting papers by throwing (an unbiased!) coin," explain the researchers.

Daniel Kennefick, a cosmologist at the University of Arkansas with a special interest in sociology, believes that the study exposes the vulnerability of peer review when referees are not accountable for their decisions. "The system provides an opportunity for referees to try to avoid embarrassment for themselves, which is not the goal at all," he says. (September 9, 2010)

The major problem, as I see it, is that peer review is sold to the public as a key determinant of quality, which it isn't and can't be, under the circumstances. Scientists know about and talk about this problem, but nothing much seems to get done about it.

(Note: "Rational" means self-serving enough to reject a paper that might draw attention away from one's own work - I guess they were looking for a polite way to put that ...)

I have written elsewhere about peer review.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

by Denyse O'Leary
ARN correspondent

A friend writes to note a new blog:

The Bubble Chamber is a new blog written by historians and philosophers of science for discussing contemporary issues of science and society through the lens of historical context and critical analysis.

Founded by the University of Toronto's Science Policy Working Group, The Bubble Chamber is a forum for those interested in a critical assessment of science in society and the development, regulation, and trajectory of science.

Much of it would certainly interest ID types; for example, Mike Thicke on "Is Sam Harris on to something: Can science answer moral questions? Thicke quotes Darwinian atheist neuroscientist Harris:

I was not suggesting that science can give us an evolutionary or neurobiological account of what people do in the name of “morality.” Nor was I merely saying that science can help us get what we want out of life. Both of these would have been quite banal claims to make (unless one happens to doubt the truth of evolution or the mind’s dependency on the brain). Rather I was suggesting that science can, in principle, help us understand what we should do and should want—and, perforce, what other people should do and want in order to live the best lives possible. My claim is that there are right and wrong answers to moral questions, just as there are right and wrong answers to questions of physics, and such answers may one day fall within reach of the maturing sciences of mind.

So what do you think? Is Sam Harris just repeating Wilson’s mistakes, or is Hume’s is-ought divide best forgotten? Can we really find new ethical principles by studying biology, psychology, or neuroscience? What would they look like? What do you think of the principles Harris proposes in his TED talk?

Good for Mike for wondering; not as Thicke as some.

(The answer, of course, is no, unless we are zombies, in which case any principles would elude us anyway.There is no "science of mind" that is proof against temptation to do what we know to be wrong, though there could be zombification.)

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

by Denyse O'Leary
ARN correspondent

Here is Clive Copus's review (23 September 2010) of Darwin skeptic James Le Fanu's Why Us?

Le Fanu writes beautifully - almost poetically, at times - but never loses sight of his underlying message. Beginning with an evocative account of the discovery of the artwork of Cro-Magnon man in a French cave, he marvels at the sudden and inexplicable emergence of mankind, with our unique powers of imagination, reasoning and abstract thought. The contrast with our primate 'cousins' should be self-evident, but the distorting lens of the Darwinian paradigm has served only to emphasise and exaggerate our similarities. Consequently, huge areas of potential research into what makes humans 'special' have been largely ignored, with disastrous consequences for the scientific enterprise.

[ ... ]

... both stunning and liberating: stunning because it is the very opposite of what scientists – working, of course, within the constraints of the Darwinian paradigm - expected to find; and liberating because it frees us from the rigid determinism of the selfish gene, with all that that implies for free will and objective moral values.

[ ... ]

... it provides the context for the author's main thesis - that cutting-edge science is providing us with an opportunity to break free of the shackles of materialist reductionism, and re-embrace the concept of the soul. In two areas in particular - genetics and neuroscience - research over the last 20 years has shown that we are much more than the sum of our brain's electrical impulses and our DNA's instructions. This is both stunning and liberating: stunning because it is the very opposite of what scientists - working, of course, within the constraints of the Darwinian paradigm - expected to find; and liberating because it frees us from the rigid determinism of the selfish gene, with all that that implies for free will and objective moral values.

Here's a bit more on Le Fanu from his site:

James Le Fanu was born in 1950 and spent his childhood in Scotland, East Africa, Yugoslavia and Cyprus. He studied the Humanities at Ampleforth College before switching to medicine, graduating from Cambridge University and the Royal London Hospital in 1974. He subsequently worked in the Renal Transplant Unit and Cardiology Departments of the Royal Free and St Mary's Hospital in London. For the past twenty years he has combined working as a doctor in general practice with contributing a weekly column to the Sunday and Daily Telegraph. He has contributed articles and reviews to The New Statesman, Spectator, GQ, The British Medical Journal and Journal of the Royal Society of Medicine. He has written several books including 'The Rise and Fall of Modern Medicine' that won the Los Angeles Prize Book Award in 2001 and 'Why Us?: How Science Rediscovered the Mystery of Ourselves' that was published in Britain and the United States in February 2009.

Two comments:

Reviewer Copus seems to think that another good book exposing Darwinism's weaknesses will help weaken it as a social theory. Not so. We might no more expect that than we might expect astrology to be weakened as a social theory by exposure of nonsense. The Toronto Star, for example - street capo for all things Darwin - has an astrologer as well, Jacqueline Biggar, .

Second, and related, thousands upon thousands of academics and others make a living - often at tax expense - fronting Darwinian nonsense and foolishness. And what makes either Copus or Le Fanu think that these people actually want to be free?

(Note:When Darwin's chihuahua, Britmag New Scientist, went after Le Fanu, he appears to have threatened the mag with Britain's libel laws. The whole affair was a bit murky at first, and I got dragged into it because I was the only other person mentioned in the article - and, as it happens, am a free speech journalist, with little use for Britain's libel laws or libel tourism generally.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

In ENV, and a press release from the new centre...In recent years, the development of Intelligent Design theory has been associated with the USA, but now a Centre for Intelligent Design has opened in the UK.

Intelligent Design (ID) theory argues that certain features of the universe and of living things are best explained by intelligent causation. As the scientific case for ID has become increasingly visible around the world, it deserves a voice in Britain.

More...

A new "Intelligent Design Applet" for Android, BlackBerry, iPad, and iPhone has been created by IDEA Center Board Member, Dr. H. Wayne House, the editor of Intelligent Design 101. The App includes links to pro-ID websites, pro-ID blog updates, and FAQs on intelligent design. For more information, visit the Intelligent Design Applet's website

Earlier this year, the work of Nir Goldman and colleagues was noted (here). Using sophisticated computer modeling tools, it was concluded that cometary impacts could generate C-N bonded oligomers that subsequently break apart to form a glycine-containing complex. This research has now been published in Nature Chemistry, resulting in a new flurry of discussion about the shock synthesis of life.

Topographic map of the Moon based on measurements from the Lunar Orbiter Laser Altimeter, showing the boundary between Oceanus Procellarum, a smooth, relatively young mare region on the western nearside (upper right), and the older, more heavily cratered highlands (center and lower left). Colors indicate increasing elevation from blue to red. Both Earth and Moon experienced the effects of impactors. (Source here)

It is known from Stanley Miller's experiments that amino acids can be synthesized in a reducing atmosphere. However, the evidence for such an atmosphere has become less convincing with time - and even a neutral atmosphere means the Miller route for generating amino acids is unproductive. Cometary impacts, however, can make this point irrelevant, as is explained by John Timmer here.

"One of the problems facing origin-of-life research is that building complex organic chemicals requires a reducing environment, but the early Earth's atmosphere is now thought to have been weakly oxidizing. None of this matters as the comet hits. A typical shockwave quickly reaches conditions where the simple compounds break down, liberating hydrogen ions. These create local reducing environments no matter what the atmosphere looks like."

We should note the nature of the computing challenge for the research team. They started with a mixture of water, methanol, ammonia, carbon monoxide and carbon dioxide. Then, as explained by Timmer:

"they ran molecular dynamics simulations of what might happen to a typical cometary mixture as a blazing hot shockwave passed through, and was followed by a rapid decompression. These were pretty elaborate calculations, with femtosecond time resolution, and molecular interactions that considered quantum effects. Simply modeling the decompression that followed a shockwave for 50 picoseconds involved about 80,000 CPU hours. They also reran the model to simulate different speeds and angles of impact, which produce different pressure/temperature combinations within the shockwave that passes through the comet."

Somehow, the leap from glycine (and amino acids in general) to life has become instinctive rather than reasoned. Nature carried a short report with the title: "Origins of life: Shock synthesis". The research however reported a route to synthesise glycine, not life! Chemistry World was overconfident in its headline: "Comet shockwaves helped stimulate life on Earth", but more nuanced with the byline: "Comet strikes could have delivered the necessary ingredients and conditions to stimulate life on Earth". The reputation of science journalism is not helped by these headlines: the idea that it is a small step from amino acids to life is fantasy! We have had many decades of serious research by very dedicated people, and this has revealed an enormous gulf between organic molecules and organic life. For more on this, go here.

Timmer's assessment of the research is probably the best that can be said:

"Right now, most scientists think that life originated in an RNA world, where proteins didn't exist, and amino acids simply acted as co-factors for some key chemical reactions. So this doesn't necessarily help us understand how life first got started. It may, however, provide some insight into how life started using amino acids in the first place, starting it on the road towards the production of proteins. If basic amino acids were plentiful, then evolution might have simply worked with what was already around."

Everyone acknowledges that cometary impacts have more potential to destroy life than to promote it, so it is worth drawing attention to the most recent study of the lunar impact craters greater than 20 km. This research drew on data gathered by the Lunar Orbiter Laser Altimeter, an instrument on board the Lunar Reconnaissance Orbiter spacecraft. The researchers explain: "These data provide a view of the global distribution of impact craters without the observational uncertainties that arose from measurement of craters on images of heterogeneous illumination condition and uneven coverage and quality." Their findings validate the hypothesis that there has been an early and a later impactor population inside the asteroid belt. The authors write: "Furthermore, it places the transition between these two populations at about the time of Orientale Basin, the last large multi-ringed basin thought to have formed ~3.8 billion years ago." The significance of this for abiogenesis advocates is that their thinking about the origin of life must be temporally constrained. They cannot reasonably postulate an origin prior to 3.9 Ga. Writing in The Daily Telegraph, Matthew Moore points out:

"Any life which may have existed on Earth 3.9 billion years ago would have been wiped out in a devastating asteroid strike, new analysis of Moon craters indicates." [. . .] "Earth and its satellite were bombarded with large asteroids during the solar system's "turbulent youth", striking new topographical maps show. The impacts would have been powerful enough to evaporate any water on our planet and destroy any early organisms."

Compare this with some reports of photosynthetic life at 3.8 Ga and with the general acceptance of life by 3.5 Ga. Life was on Earth in the Early Archaean. The resultant time constraints undermine all chance-based scenarios of abiogenesis. This leaves us with law-based explanations (which are totally unable to account for biological information) or design-based explanations. The latter option is the direction where science is leading us.

Synthesis of glycine-containing complexes in impacts of comets on early Earth
Nir Goldman, Evan J. Reed, Laurence E. Fried, I.-F. William Kuo & Amitesh Maiti.
Nature Chemistry, (September 2010) | doi:10.1038/nchem.827

Delivery of prebiotic compounds to early Earth from an impacting comet is thought to be an unlikely mechanism for the origins of life because of unfavourable chemical conditions on the planet and the high heat from impact. In contrast, we find that impact-induced shock compression of cometary ices followed by expansion to ambient conditions can produce complexes that resemble the amino acid glycine. Our ab initio molecular dynamics simulations show that shock waves drive the synthesis of transient C-N bonded oligomers at extreme pressures and temperatures. On post impact quenching to lower pressures, the oligomers break apart to form a metastable glycine-containing complex. We show that impact from cometary ice could possibly yield amino acids by a synthetic route independent of the pre-existing atmospheric conditions and materials on the planet.

See also:

Mitchinson, A. Origins of life: Shock synthesis, Nature, 467, 281, (16 September 2010) | doi:10.1038/467281a

Head, J.W. et al., Global Distribution of Large Lunar Craters: Implications for Resurfacing and Impactor Populations, Science, 329, 17 September 2010: 1504-1507 | DOI: 10.1126/science.1195050

by Denyse O'Leary
ARN correspondent

Adapting to Darkness: How Behavioral and Genetic Changes Helped Cavefish Survive Extreme Environment

Becoming eyeless is an adaptation of sorts, no?

ScienceDaily (Sep. 15, 2010) - University of Maryland biologists have identified how changes in both behavior and genetics led to the evolution of the Mexican blind cavefish (Astyanax mexicanus) from its sighted, surface-dwelling ancestor. In research published in the August 12, 2010 online edition of the journal Current Biology, Professor William Jeffery, together with postdoctoral associates Masato Yoshizawa, and Å pela Goricki, and Assistant Professor Daphne Soares in the Department of Biology, provide new information that shows how behavioral and genetic traits coevolved to compensate for the loss of vision in cavefish and to help them find food in darkness.

This is the first time that a clear link has been identified between behavior, genetics, and evolution in Mexican blind cavefish, which are considered an excellent model for studying evolution.

Actually, to the extent that the cavefish lost a trait rather than gained one, what we are studying here is devolution rather than evolution. Just how the main different types of eye evolved is a fascinating topic. How traits can get lost is interesting too, but not as relevant to the question of how great gains in information really occur.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

by Denyse O'Leary
ARN correspondent

At Intelligent Life (Autumn 2010), in "LIMITS OF SCIENCE," Anthony Gottlieb asks,"Plenty of today's scientific theories will one day be discredited. So should we be sceptical of science itself?":

At the end of her book "Science: A Four Thousand Year History" (2009), Patricia Fara of Cambridge University wrote that "there can be no cast-iron guarantee that the cutting-edge science of today will not represent the discredited alchemy of tomorrow". This is surely an understatement. If the past is any guide-and what else could be? - plenty of today's science will be discredited in future. There is no reason to think that today's practitioners are uniquely immune to the misconceptions, hasty generalisations, fads and hubris that marked most of their predecessors. Although the best ideas of Copernicus, Galileo, Newton, Boyle, Darwin, Einstein and others have stood the test of time and taken their place in the permanent corpus of knowledge, error remains inherent in the enterprise of science. This is because interesting theories always go beyond the data that they seek to explain, and because science is made by people. Examples from recent decades of scientific consensus that turned out to be wrong range from the local to the largest possible scale: acid rain was not destroying forests in Germany in the 1980s, as it was said to have been, and the expansion of the universe has not been slowing down, as cosmologists used to think it was.

Physicists, in particular, have long believed themselves to be on the verge of explaining almost everything. In 1894 Albert Michelson, the first American to get a Nobel prize in science, said that all the main laws and facts of physics had already been discovered. In 1928 Max Born, another Nobel prize-winner, said that physics would be completed in about six months' time. In 1988, in his bestselling "A Brief History of Time", the cosmologist Stephen Hawking wrote that "we may now be near the end of the search for the ultimate laws of nature." Now, in the newly published "The Grand Design", Hawking paints a picture of the universe that is "different ... from the picture we might have painted just a decade or two ago". In the long run, physicists are, no doubt, getting closer and closer to the truth. But you can never be sure when the long run has arrived. And in the short run-to adapt Keynes's proverb-we are often all wrong.

Most laymen probably assume that the 350-year-old institution of "peer review", which acts as a gatekeeper to publication in scientific journals, involves some attempt to check the articles that see the light of day. In fact they are rarely checked for accuracy, and, as a study for the Fraser Institute, a Canadian think-tank, reported last year, "the data and computational methods are so seldom disclosed that post-publication verification is equally rare." Journals will usually consider only articles that present positive and striking results, and scientists need constantly to publish in order to keep their careers alive. So it is that, like the late comedian Danny Kaye, professional scientists sometimes get their exercise by jumping to conclusions. Historians of science call this bias the "file-drawer problem": if a set of experiments produces a result contrary to what the team needs to find, it ends up filed away, and the world never finds out about it.

Yes, indeed, and many people - especially older people - either know or sense this sort of thing. The "theory of everything problem is a huge handicap to getting taken seriously. It is evolutionary psychology (how your inner ape runs your life), for example, that makes Darwin's theory sound ridiculous in many people's eyes, not the bare bones theory itself, which is at least debatable:

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

by Denyse O'Leary
ARN correspondent

From ScienceDaily, we learn,

Why 'Scientific Consensus' Fails to Persuade

(Sep. 14, 2010) If you are like most people, the answer is likely to be, "it
depends." What it depends on, a recent study found, is not whether the position that scientist takes is consistent with the one endorsed by a National Academy. Instead, it is likely to depend on whether the position the scientist takes is consistent with the one believed by most people who share your cultural values.

This was the finding of a recent study conducted by Yale University law professor Dan Kahan, University of Oklahoma political science professor Hank Jenkins-Smith and George Washington University law professor Donald Braman that sought to understand why members of the public are sharply and persistently divided on matters on which expert scientists largely agree.

An interesting article, but a little too self-pleasing for my taste. The reason people doubt expert science (or other) consensus is that they often know reasons why the consensus might not be correct, not just because they are biased but the experts are not. Sometimes a consensus is just a herd of independent minds, bellowing noisily as they gallop off a cliff. I am sixty years old, and it is interesting to reflect on all the expert opinion extant in my youth, and what happened to it.

Toronto-based Canadian journalist Denyse O'Leary (www.designorchance.com) is the author of the multiple award-winning By Design or by Chance? (Augsburg Fortress 2004), an overview of the intelligent design controversy. She was named CBA Canada's Recommended Author of the Year in 2005 and is co-author, with Montreal neuroscientist Mario Beauregard, of The Spiritual Brain: A neuroscientist's case for the existence of the soul (Harper 2007).

by Denyse O'Leary
ARN correspondent

According to Larry O'Hanlon at Discovery News, "Ancient animal explosion gets bigger with new finds" (9/9/2010),

At least eight new kinds of Earth's earliest animals from the mysterious and controversial Cambrian Explosion have been discovered in a unexpected section of ancient rock 30 miles from the famous Burgess Shale of Canada. The discovery suggests such old, rare fossils are more common than previously thought.

Like the fossils of the original Burgess Shale, the new discoveries are remarkable because they preserve features of animals which had no hard parts — like gills and eyes — and remained intact for more than half a billion years.

That's a time when animals evolved from being very small, simple organisms into a wildly creative, explosive variety of sometimes bizarre creatures.

These were culled by natural selection over time, leaving the more familiar main animal groups we see today.

I don'